The document discusses protein backbone flexibility and the Ramachandran plot. It provides information on:
1) The phi and psi torsion angles that describe rotations around peptide bonds in the protein backbone and allow for different protein conformations.
2) How the Ramachandran plot maps allowed and disallowed phi-psi angle combinations based on steric clashes, and observed combinations in real proteins.
3) The plot serves as an indicator of protein structure quality by showing if residues fall in allowed regions. Understanding phi-psi angles helps predict protein folding.
The document discusses the Ramachandran plot, which shows statistically probable combinations of the phi and psi backbone torsion angles in proteins. It describes how these two angles describe rotations around bonds in the polypeptide backbone and influence protein folding. The plot reveals allowed and disallowed regions based on steric clashes between atoms at different angle combinations. Common structures like alpha helices and beta sheets correspond to allowed regions in the plot.
The document summarizes Ramachandran plots, which visualize backbone dihedral angles ψ against φ of amino acid residues in protein structures. Ramachandran plots show sterically allowed and disallowed conformations based on calculations using van der Waals radii and bond angles. Specific regions of the plot correspond to different secondary structures like alpha helices and beta sheets. The plots can also be used to validate protein structures by comparing observed dihedral angles to expected allowed regions.
Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
This document discusses Ramachandran plots, which are used to visualize protein backbone structures and calculate possible phi and psi bond angles in amino acid residues. Ramachandran plots show favored, allowed, and generously allowed regions for different bond angles based on analysis of crystal structure data and distributions of over 9,000 amino acid residues. Two high-density areas correspond to alpha-helices and beta-structures. Glycine and proline residues have fewer allowed regions due to their side chain properties.
This document discusses the limits on rotation in protein backbones and defines the psi (ψ) and phi (φ) angles. It introduces the Ramachandran plot, which maps allowed combinations of ψ and φ angles based on steric constraints. The plot reveals preferred regions that correspond to common secondary structures like alpha helices and beta sheets. Understanding the steric limits on individual amino acid residues provides insight into how proteins fold into their specific three-dimensional shapes.
The document discusses different forms of DNA structure that can be adopted based on environmental conditions. The main forms discussed are B-DNA, A-DNA, Z-DNA, C-DNA, D-DNA and E-DNA. B-DNA is the most common form, having a right-handed double helix structure with 10 base pairs per turn. A-DNA and Z-DNA are also double helical but have different structural characteristics than B-DNA such as base pair spacing and groove size. The various forms arise in response to changes in humidity, ionic conditions and DNA sequence composition.
1. The document discusses models of homologous recombination including the Holliday model and the double-strand break repair model. It describes the key steps and proteins involved in each model.
2. Recombination involves the breakage and rejoining of DNA. In eukaryotes, the MRN/X complex processes DNA breaks. The Rad51 and Rad54 proteins then facilitate strand invasion and D-loop formation during homologous pairing.
3. Homologous recombination proteins from bacteria and eukaryotes catalyze different steps of the process. In E. coli, RecBCD introduces breaks and generates single strands for RecA to perform strand exchange, while RuvAB and Ruv
The document discusses the Ramachandran plot, which shows statistically probable combinations of the phi and psi backbone torsion angles in proteins. It describes how these two angles describe rotations around bonds in the polypeptide backbone and influence protein folding. The plot reveals allowed and disallowed regions based on steric clashes between atoms at different angle combinations. Common structures like alpha helices and beta sheets correspond to allowed regions in the plot.
The document summarizes Ramachandran plots, which visualize backbone dihedral angles ψ against φ of amino acid residues in protein structures. Ramachandran plots show sterically allowed and disallowed conformations based on calculations using van der Waals radii and bond angles. Specific regions of the plot correspond to different secondary structures like alpha helices and beta sheets. The plots can also be used to validate protein structures by comparing observed dihedral angles to expected allowed regions.
Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
This document discusses Ramachandran plots, which are used to visualize protein backbone structures and calculate possible phi and psi bond angles in amino acid residues. Ramachandran plots show favored, allowed, and generously allowed regions for different bond angles based on analysis of crystal structure data and distributions of over 9,000 amino acid residues. Two high-density areas correspond to alpha-helices and beta-structures. Glycine and proline residues have fewer allowed regions due to their side chain properties.
This document discusses the limits on rotation in protein backbones and defines the psi (ψ) and phi (φ) angles. It introduces the Ramachandran plot, which maps allowed combinations of ψ and φ angles based on steric constraints. The plot reveals preferred regions that correspond to common secondary structures like alpha helices and beta sheets. Understanding the steric limits on individual amino acid residues provides insight into how proteins fold into their specific three-dimensional shapes.
The document discusses different forms of DNA structure that can be adopted based on environmental conditions. The main forms discussed are B-DNA, A-DNA, Z-DNA, C-DNA, D-DNA and E-DNA. B-DNA is the most common form, having a right-handed double helix structure with 10 base pairs per turn. A-DNA and Z-DNA are also double helical but have different structural characteristics than B-DNA such as base pair spacing and groove size. The various forms arise in response to changes in humidity, ionic conditions and DNA sequence composition.
1. The document discusses models of homologous recombination including the Holliday model and the double-strand break repair model. It describes the key steps and proteins involved in each model.
2. Recombination involves the breakage and rejoining of DNA. In eukaryotes, the MRN/X complex processes DNA breaks. The Rad51 and Rad54 proteins then facilitate strand invasion and D-loop formation during homologous pairing.
3. Homologous recombination proteins from bacteria and eukaryotes catalyze different steps of the process. In E. coli, RecBCD introduces breaks and generates single strands for RecA to perform strand exchange, while RuvAB and Ruv
DNA repair is a collection of processes cells use to identify and correct damage to DNA. Failure to repair damaged DNA leads to mutations, which are permanent changes in the DNA sequence. There are several types of DNA damage including mismatches, modified DNA bases, and single or double strand breaks. Cells use multiple repair pathways like direct reversal, base excision repair, nucleotide excision repair, recombination repair, and translesion DNA synthesis to fix different types of DNA damage. Homologous recombination repairs double strand breaks by exchanging DNA between similar molecules, while site-specific and transposon recombination involve movement of DNA between defined sequences.
G.N. Ramachandran developed the Ramachandran plot in 1963 to visualize allowed backbone dihedral angles (phi and psi) of amino acid residues in protein structures. The plot shows sterically allowed and disallowed regions for phi-psi torsion angles based on collisions between atoms treated as hard spheres. It has since been used for protein structure validation and improvement of structure determination methods. The favored regions correspond to common secondary structure motifs like alpha helices and beta sheets.
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
Riboswitches are RNA elements found in the 5' untranslated region of mRNA that can bind to specific metabolites and undergo a conformational change to regulate gene expression. They are classified based on the ligand they bind and their secondary structure. Examples include TPP, lysine, glycine, FMN, purine, and cobalamin riboswitches. A riboswitch has two domains - an aptamer domain that binds the ligand and an expression platform domain that can adopt two structures to control transcription or translation. Binding of a metabolite can induce formation of a terminator stem loop to terminate transcription, mask the ribosome binding site to inhibit translation initiation, or trigger self-cleavage of the mRNA.
A suppressor mutation counters the effects of an original mutation by restoring the wild-type phenotype. There are two main types of suppressor mutations: intragenic mutations occur within the same gene and restore function through alternate amino acid substitutions, while intergenic mutations occur elsewhere in the genome and restore function through interacting gene products. Suppressor mutations are useful for studying protein-protein interactions and dissecting biological pathways.
This document discusses different types of RNA, including messenger RNA, transfer RNA, and ribosomal RNA. It describes:
1) Messenger RNA carries genetic information from DNA in the nucleus to the cytoplasm for protein production. Messenger RNA can be polycistronic, containing information for multiple proteins, or monocistronic, containing information for a single protein.
2) Transfer RNA transports amino acids to the ribosome during protein translation based on the messenger RNA code. It has a cloverleaf secondary structure and L-shape tertiary structure.
3) Ribosomal RNA is a structural component of ribosomes and facilitates protein synthesis by decoding messenger RNA and interacting with transfer RNA. It comprises the large and
I have tried to make a precise presentation on protein transport, targeting and sorting into organelle's other than nucleus. Hope this might help you. Comments are welcome.
This document summarizes homologous recombination in eukaryotes and bacteria. In eukaryotes, homologous recombination repairs double-strand DNA breaks through either the double-strand break repair (DSBR) pathway or synthesis-dependent strand annealing (SDSA) pathway. The DSBR pathway forms double Holliday junctions that are resolved to result in crossover or non-crossover products. In bacteria, the RecBCD pathway repairs double-strand breaks and the RecF pathway repairs single-strand gaps. Both pathways involve strand invasion and branch migration to facilitate homologous recombination.
The document discusses Ramachandran plots, which are used to visualize allowed regions of dihedral angles phi and psi in protein backbone structures. Ramachandran plots show amino acid residues as dots in a two-dimensional map based on their phi and psi angles. Most residues cluster in favored regions corresponding to alpha helices and beta sheets. The document outlines how Ramachandran plots are constructed and analyzed using various software, and their applications in validating protein structures and understanding relationships between structure and amino acid sequence.
RNA splicing is a process where introns are removed from precursor messenger RNA (pre-mRNA) and exons are joined together to produce mature mRNA. It occurs in the nucleus and is essential for eukaryotes to produce proteins. The spliceosome, a large complex of RNA and proteins, facilitates two transesterification reactions that remove introns and ligate exons. RNA splicing generates protein diversity through alternative splicing and is important for cellular functions and disease processes.
DNA topology studies the geometric properties and spatial relationships of DNA that are unaffected by changes in shape or size. It includes phenomena like supercoiling, knots, and catenanes that involve the linking and twisting of the two DNA strands. DNA topology is characterized by parameters like the linking number, which represents the number of times the two strands are twisted around each other. Enzymes called topoisomerases regulate DNA topology by introducing temporary breaks in the DNA strands to allow strand passage and control supercoiling levels.
1. DNA can be damaged through various mechanisms including base substitutions during replication, base changes due to instability, and damage from chemicals and environmental agents.
2. This document describes different types of DNA damage including mismatches, missing or altered bases, single and double strand breaks, and cross-linking.
3. DNA repair mechanisms are discussed, including mismatch repair, removal of incorrect bases by uracil glycosylase, and light-dependent and light-independent repair of thymine dimers through excision and recombinational repair.
The document discusses protein folding, which is the process by which a polypeptide chain folds into its characteristic and functional three-dimensional structure. It describes the four levels of protein structure: primary, secondary, tertiary, and quaternary. Key drivers of folding are the hydrophobic effect and formation of hydrogen bonds. Chaperone proteins assist in protein folding in vivo. Factors such as mutations, errors in synthesis, environmental stresses, and aging can cause proteins to misfold and aggregate, which is associated with various diseases. Cells use molecular chaperones and protein degradation systems to prevent aggregation, but these become less effective with age.
This document discusses different types of chaperone proteins. It begins by explaining that chaperones assist other proteins in folding correctly by interacting with unfolded or misfolded proteins. The main types discussed are molecular chaperones like Hsp70 and Hsp90, and chaperonins. Hsp70 binds to hydrophobic regions of unfolded proteins to prevent aggregation, while Hsp90 helps activate client proteins. Chaperonins form folding chambers and there are two groups - group 1 found in prokaryotes and organelles, and group 2 in eukaryotes and archaea. Specific examples of chaperone homologs in different organisms are also provided.
The Ramachandran plot maps the allowed regions of phi and psi dihedral angles in protein backbone structures. It revealed that phi and psi angles are restricted to specific regions to avoid steric clashes between atoms. The main allowed regions correspond to alpha-helical and beta-sheet conformations. The plot is an important tool for analyzing protein structures and validating predicted folds based on expected phi and psi angles.
This ppt will help you get through the complete topic for RAMACHANDRAN PLOT in detail .
for detailed explanation , watch the lecture on my youtube channel - BOTANY INSIDER
Regulation of gene expression in eukaryotesSuchittaU
This document summarizes gene regulation in eukaryotes. It discusses how gene expression is regulated at multiple levels, including transcription, RNA processing, and intracellular/intercellular signaling. Key points include: (1) Gene expression is controlled by transcription factors binding to promoter and enhancer regions; (2) Eukaryotic gene expression involves RNA splicing and alternative splicing of exons; and (3) The Britten-Davidson model proposes that sensor genes control integrator genes which regulate sets of producer genes in response to signals.
Levels of protein structure include primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structure involves hydrogen bonding between amino acids to form alpha helices and beta sheets. Tertiary structure describes how secondary structures fold in 3D space, stabilized by noncovalent bonds. Quaternary structure involves the interaction of multiple polypeptide chains. Protein folding is assisted by chaperone proteins and errors can lead to diseases like Alzheimer's and prion diseases.
Levels of protein structure include primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structure involves hydrogen bonding between amino acids to form alpha helices and beta sheets. Tertiary structure describes how secondary structures fold in 3D space, stabilized by noncovalent bonds. Quaternary structure involves the interaction of multiple polypeptide chains. Protein folding is assisted by chaperone proteins and errors can lead to diseases like Alzheimer's and prion diseases.
DNA repair is a collection of processes cells use to identify and correct damage to DNA. Failure to repair damaged DNA leads to mutations, which are permanent changes in the DNA sequence. There are several types of DNA damage including mismatches, modified DNA bases, and single or double strand breaks. Cells use multiple repair pathways like direct reversal, base excision repair, nucleotide excision repair, recombination repair, and translesion DNA synthesis to fix different types of DNA damage. Homologous recombination repairs double strand breaks by exchanging DNA between similar molecules, while site-specific and transposon recombination involve movement of DNA between defined sequences.
G.N. Ramachandran developed the Ramachandran plot in 1963 to visualize allowed backbone dihedral angles (phi and psi) of amino acid residues in protein structures. The plot shows sterically allowed and disallowed regions for phi-psi torsion angles based on collisions between atoms treated as hard spheres. It has since been used for protein structure validation and improvement of structure determination methods. The favored regions correspond to common secondary structure motifs like alpha helices and beta sheets.
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
Riboswitches are RNA elements found in the 5' untranslated region of mRNA that can bind to specific metabolites and undergo a conformational change to regulate gene expression. They are classified based on the ligand they bind and their secondary structure. Examples include TPP, lysine, glycine, FMN, purine, and cobalamin riboswitches. A riboswitch has two domains - an aptamer domain that binds the ligand and an expression platform domain that can adopt two structures to control transcription or translation. Binding of a metabolite can induce formation of a terminator stem loop to terminate transcription, mask the ribosome binding site to inhibit translation initiation, or trigger self-cleavage of the mRNA.
A suppressor mutation counters the effects of an original mutation by restoring the wild-type phenotype. There are two main types of suppressor mutations: intragenic mutations occur within the same gene and restore function through alternate amino acid substitutions, while intergenic mutations occur elsewhere in the genome and restore function through interacting gene products. Suppressor mutations are useful for studying protein-protein interactions and dissecting biological pathways.
This document discusses different types of RNA, including messenger RNA, transfer RNA, and ribosomal RNA. It describes:
1) Messenger RNA carries genetic information from DNA in the nucleus to the cytoplasm for protein production. Messenger RNA can be polycistronic, containing information for multiple proteins, or monocistronic, containing information for a single protein.
2) Transfer RNA transports amino acids to the ribosome during protein translation based on the messenger RNA code. It has a cloverleaf secondary structure and L-shape tertiary structure.
3) Ribosomal RNA is a structural component of ribosomes and facilitates protein synthesis by decoding messenger RNA and interacting with transfer RNA. It comprises the large and
I have tried to make a precise presentation on protein transport, targeting and sorting into organelle's other than nucleus. Hope this might help you. Comments are welcome.
This document summarizes homologous recombination in eukaryotes and bacteria. In eukaryotes, homologous recombination repairs double-strand DNA breaks through either the double-strand break repair (DSBR) pathway or synthesis-dependent strand annealing (SDSA) pathway. The DSBR pathway forms double Holliday junctions that are resolved to result in crossover or non-crossover products. In bacteria, the RecBCD pathway repairs double-strand breaks and the RecF pathway repairs single-strand gaps. Both pathways involve strand invasion and branch migration to facilitate homologous recombination.
The document discusses Ramachandran plots, which are used to visualize allowed regions of dihedral angles phi and psi in protein backbone structures. Ramachandran plots show amino acid residues as dots in a two-dimensional map based on their phi and psi angles. Most residues cluster in favored regions corresponding to alpha helices and beta sheets. The document outlines how Ramachandran plots are constructed and analyzed using various software, and their applications in validating protein structures and understanding relationships between structure and amino acid sequence.
RNA splicing is a process where introns are removed from precursor messenger RNA (pre-mRNA) and exons are joined together to produce mature mRNA. It occurs in the nucleus and is essential for eukaryotes to produce proteins. The spliceosome, a large complex of RNA and proteins, facilitates two transesterification reactions that remove introns and ligate exons. RNA splicing generates protein diversity through alternative splicing and is important for cellular functions and disease processes.
DNA topology studies the geometric properties and spatial relationships of DNA that are unaffected by changes in shape or size. It includes phenomena like supercoiling, knots, and catenanes that involve the linking and twisting of the two DNA strands. DNA topology is characterized by parameters like the linking number, which represents the number of times the two strands are twisted around each other. Enzymes called topoisomerases regulate DNA topology by introducing temporary breaks in the DNA strands to allow strand passage and control supercoiling levels.
1. DNA can be damaged through various mechanisms including base substitutions during replication, base changes due to instability, and damage from chemicals and environmental agents.
2. This document describes different types of DNA damage including mismatches, missing or altered bases, single and double strand breaks, and cross-linking.
3. DNA repair mechanisms are discussed, including mismatch repair, removal of incorrect bases by uracil glycosylase, and light-dependent and light-independent repair of thymine dimers through excision and recombinational repair.
The document discusses protein folding, which is the process by which a polypeptide chain folds into its characteristic and functional three-dimensional structure. It describes the four levels of protein structure: primary, secondary, tertiary, and quaternary. Key drivers of folding are the hydrophobic effect and formation of hydrogen bonds. Chaperone proteins assist in protein folding in vivo. Factors such as mutations, errors in synthesis, environmental stresses, and aging can cause proteins to misfold and aggregate, which is associated with various diseases. Cells use molecular chaperones and protein degradation systems to prevent aggregation, but these become less effective with age.
This document discusses different types of chaperone proteins. It begins by explaining that chaperones assist other proteins in folding correctly by interacting with unfolded or misfolded proteins. The main types discussed are molecular chaperones like Hsp70 and Hsp90, and chaperonins. Hsp70 binds to hydrophobic regions of unfolded proteins to prevent aggregation, while Hsp90 helps activate client proteins. Chaperonins form folding chambers and there are two groups - group 1 found in prokaryotes and organelles, and group 2 in eukaryotes and archaea. Specific examples of chaperone homologs in different organisms are also provided.
The Ramachandran plot maps the allowed regions of phi and psi dihedral angles in protein backbone structures. It revealed that phi and psi angles are restricted to specific regions to avoid steric clashes between atoms. The main allowed regions correspond to alpha-helical and beta-sheet conformations. The plot is an important tool for analyzing protein structures and validating predicted folds based on expected phi and psi angles.
This ppt will help you get through the complete topic for RAMACHANDRAN PLOT in detail .
for detailed explanation , watch the lecture on my youtube channel - BOTANY INSIDER
Regulation of gene expression in eukaryotesSuchittaU
This document summarizes gene regulation in eukaryotes. It discusses how gene expression is regulated at multiple levels, including transcription, RNA processing, and intracellular/intercellular signaling. Key points include: (1) Gene expression is controlled by transcription factors binding to promoter and enhancer regions; (2) Eukaryotic gene expression involves RNA splicing and alternative splicing of exons; and (3) The Britten-Davidson model proposes that sensor genes control integrator genes which regulate sets of producer genes in response to signals.
Levels of protein structure include primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structure involves hydrogen bonding between amino acids to form alpha helices and beta sheets. Tertiary structure describes how secondary structures fold in 3D space, stabilized by noncovalent bonds. Quaternary structure involves the interaction of multiple polypeptide chains. Protein folding is assisted by chaperone proteins and errors can lead to diseases like Alzheimer's and prion diseases.
Levels of protein structure include primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structure involves hydrogen bonding between amino acids to form alpha helices and beta sheets. Tertiary structure describes how secondary structures fold in 3D space, stabilized by noncovalent bonds. Quaternary structure involves the interaction of multiple polypeptide chains. Protein folding is assisted by chaperone proteins and errors can lead to diseases like Alzheimer's and prion diseases.
The document provides information on protein structure and function including:
- Proteins have a variety of functions including catalysis, structure, transport, signaling, and storage.
- The central dogma of molecular biology describes how DNA is transcribed into mRNA and then translated into proteins.
- Protein structure is determined by each protein's unique amino acid sequence and how they fold into secondary structures like alpha helices and beta sheets.
- The alpha helix and beta sheet are the most common secondary structures, stabilized by hydrogen bonds between amino acids in the backbone.
RAMACHANDRAN PLOT One is to show in principle which values of and angles are ...406SAKSHIPRIYA
This presentation is based on Ramachandran plot, which uses computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations. Plotting the torsional angles in this way graphically shows which combination of angles are possible.
The Ramachandran plot provides a graphical representation of allowed phi and psi dihedral angles for protein backbone structures. It revealed that most phi-psi combinations are sterically prohibited except for certain allowed regions. The plot remains an important tool for validating protein structures determined experimentally or through modeling, as structures with residues falling in forbidden regions likely have low quality. It also allows prediction of secondary structure based on characteristic phi-psi angles of different structures like alpha helices and beta sheets.
The document describes the four levels of protein structure:
1) Primary structure is the linear sequence of amino acids joined by peptide bonds.
2) Secondary structure involves localized patterns like alpha helices and beta sheets formed by hydrogen bonds.
3) Tertiary structure is the overall 3D shape of the polypeptide chain formed by interactions like disulfide bridges, hydrogen bonds, and hydrophobic interactions.
4) Quaternary structure refers to complexes of multiple polypeptide subunits.
Gives in detail primary, secondary, tertiary and Quaternary structure of proteins. Gives classification of secondary structure: alpha helix, beta pleated sheet and different types of tight turns and explains most commonly found tight turn in proteins i.e. beta turn. Briefs about the Ramachandran plot of proteins, dihedral or torsion angles and explains why glycine and proline act as alpha helix breakers. Explains tertiary structure of proteins and different covalent and non covalent bonds in the tertiary structure and relative importance of these bonding interactions. Details about the quaternary structure of proteins and explains why hemoglobin is a quaternary protein and insulin is not.
This lecture discusses protein structure and function, specifically focusing on secondary structure elements. It covers the conformations of peptide groups including cis and trans conformations, and dihedral angles phi and psi. Common secondary structures like alpha helices, beta sheets, and turns are described in detail. Alpha helices are stabilized by hydrogen bonds between amino acids four residues apart in the sequence. Beta sheets can be antiparallel or parallel depending on the direction of hydrogen bonding between strands. Turns and loops allow changes in the peptide chain direction. Amino acids have different preferences for forming these secondary structures.
I shikha popali and my colleague harshpal singh wahi presents a presentation "RECENT DEVELOPMENT IN DRUG DESIGN AND DISCOVERY " A detail account on protein structure is given
The document discusses various topics related to protein structure and function. It defines different types of bonds in proteins including peptide bonds, disulfide bonds, and hydrogen bonds. It describes the 20 common amino acids that make up proteins and different secondary structures such as alpha helices and beta sheets. It discusses the four levels of protein structure - primary, secondary, tertiary, and quaternary structure. It also covers protein folding driven by hydrophobic interactions and hydrogen bonding, as well as denaturation of proteins.
This document discusses the structure of proteins at different levels, including primary, secondary, tertiary and quaternary structure. It explains that primary structure is the amino acid sequence, and secondary structure includes alpha helices and beta sheets formed by hydrogen bonding. Tertiary structure involves the folding of secondary structure elements into the final three-dimensional shape. The document outlines methods for determining primary structure and describes concepts like the Ramachandran plot that show allowed phi and psi angles. It provides examples of common motifs in tertiary structure and defines domains.
The document discusses biomolecules and bioenergetics. It covers proteins, including their structure at various levels (primary, secondary, tertiary, quaternary), amino acids, and how protein structure is determined. It also discusses concepts of free energy, endergonic/exergonic reactions, and energy-rich compounds like ATP. The levels of protein structure - from the amino acid sequence to 3D shape - are explained in detail through primary, secondary, tertiary, and quaternary structure.
This document discusses the structure of proteins at various levels:
1) Primary structure is the amino acid sequence of a polypeptide chain.
2) Secondary structure includes alpha helices and beta pleated sheets formed by hydrogen bonding between amino acids in the backbone.
3) Tertiary structure is the three-dimensional folding of the entire polypeptide chain, stabilized by interactions between amino acid side chains.
4) Quaternary structure refers to the association of multiple polypeptide subunits in a protein.
The document outlines techniques like X-ray crystallography and NMR that are used to determine protein structures at high resolution.
Protein structures determine their functions. There are four levels of protein structure:
1) Primary structure is the amino acid sequence
2) Secondary structure involves local patterns like alpha helices and beta sheets
3) Tertiary structure describes the overall 3D shape formed by secondary structures
4) Quaternary structure refers to the arrangement of multiple polypeptide chains
The most common secondary structures are alpha helices, stabilized by hydrogen bonds between amino acids i and i+4, and beta sheets formed by hydrogen bonding between strands. Protein structure enables functions like catalysis, transport, and information transfer.
The document discusses the Ramachandran plot, which is a plot of the phi (φ) angle versus the psi (ψ) angle of amino acid residues in protein structures. It explains that these two angles are limited by steric constraints from the atoms in the protein backbone. The allowed and disallowed regions in the Ramachandran plot correspond to conformations where backbone atoms are too close or clashing versus conformations where they have sufficient space. Most protein structures fall within the allowed regions, helping explain their stable secondary structures.
Structure of protiens and the applied aspectsMohit Adhikary
The slides explain the structures of proteins, the bond stabilizing the structure of amino acids, the different types of protein structures, the applied aspects and the newer advances in the protein structure.
Strategies for Effective Upskilling is a presentation by Chinwendu Peace in a Your Skill Boost Masterclass organisation by the Excellence Foundation for South Sudan on 08th and 09th June 2024 from 1 PM to 3 PM on each day.
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptxEduSkills OECD
Iván Bornacelly, Policy Analyst at the OECD Centre for Skills, OECD, presents at the webinar 'Tackling job market gaps with a skills-first approach' on 12 June 2024
हिंदी वर्णमाला पीपीटी, hindi alphabet PPT presentation, hindi varnamala PPT, Hindi Varnamala pdf, हिंदी स्वर, हिंदी व्यंजन, sikhiye hindi varnmala, dr. mulla adam ali, hindi language and literature, hindi alphabet with drawing, hindi alphabet pdf, hindi varnamala for childrens, hindi language, hindi varnamala practice for kids, https://www.drmullaadamali.com
How to Make a Field Mandatory in Odoo 17Celine George
In Odoo, making a field required can be done through both Python code and XML views. When you set the required attribute to True in Python code, it makes the field required across all views where it's used. Conversely, when you set the required attribute in XML views, it makes the field required only in the context of that particular view.
ISO/IEC 27001, ISO/IEC 42001, and GDPR: Best Practices for Implementation and...PECB
Denis is a dynamic and results-driven Chief Information Officer (CIO) with a distinguished career spanning information systems analysis and technical project management. With a proven track record of spearheading the design and delivery of cutting-edge Information Management solutions, he has consistently elevated business operations, streamlined reporting functions, and maximized process efficiency.
Certified as an ISO/IEC 27001: Information Security Management Systems (ISMS) Lead Implementer, Data Protection Officer, and Cyber Risks Analyst, Denis brings a heightened focus on data security, privacy, and cyber resilience to every endeavor.
His expertise extends across a diverse spectrum of reporting, database, and web development applications, underpinned by an exceptional grasp of data storage and virtualization technologies. His proficiency in application testing, database administration, and data cleansing ensures seamless execution of complex projects.
What sets Denis apart is his comprehensive understanding of Business and Systems Analysis technologies, honed through involvement in all phases of the Software Development Lifecycle (SDLC). From meticulous requirements gathering to precise analysis, innovative design, rigorous development, thorough testing, and successful implementation, he has consistently delivered exceptional results.
Throughout his career, he has taken on multifaceted roles, from leading technical project management teams to owning solutions that drive operational excellence. His conscientious and proactive approach is unwavering, whether he is working independently or collaboratively within a team. His ability to connect with colleagues on a personal level underscores his commitment to fostering a harmonious and productive workplace environment.
Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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How to Setup Warehouse & Location in Odoo 17 InventoryCeline George
In this slide, we'll explore how to set up warehouses and locations in Odoo 17 Inventory. This will help us manage our stock effectively, track inventory levels, and streamline warehouse operations.
This document provides an overview of wound healing, its functions, stages, mechanisms, factors affecting it, and complications.
A wound is a break in the integrity of the skin or tissues, which may be associated with disruption of the structure and function.
Healing is the body’s response to injury in an attempt to restore normal structure and functions.
Healing can occur in two ways: Regeneration and Repair
There are 4 phases of wound healing: hemostasis, inflammation, proliferation, and remodeling. This document also describes the mechanism of wound healing. Factors that affect healing include infection, uncontrolled diabetes, poor nutrition, age, anemia, the presence of foreign bodies, etc.
Complications of wound healing like infection, hyperpigmentation of scar, contractures, and keloid formation.
2. Proteins And Backbone Flexibility
Proteins are most abundant organic
molecules of living system.
They constitute 70% of total dry weight.
They form fundamental basis of structure &
function of life.
Proteins are nitrogenous macromolecules
composed of many amino acids.
3. Peptide bond formation
• Alpha carboxyl group of amino acid with forms a
covalent peptide bond with alpha amino group of
other amino acid by removal of a molecule of
water.
• This results in di-peptide , repetition of this
process generates polypeptide or protein of
specific amino acid sequence.
• Polypeptide backbone is repeating sequence of
N-C-C-N-C-C…. In peptide bond, side chain or R-
group isn’t a part of backbone or peptide bond.
4.
5.
6. Overview of protein structure
• Configuration-Geometric relationship
between a given set of atoms.
• Conformation-Spatial arrangement of atoms
in a protein.
• Thermodynamically most stable conformation
exist . Stabilized largely by weak interactions.
• Stability-Tendency to maintain a particular
conformation.
• Conformation is stabilized by disulfide bonds
and non covalent forces.
7. Structures of proteins
• Primary structure(determined by covalent bonds)
• Secondary structure
• Tertiary structure
• Quaternary structure
• Secondary ,tertiary, quaternary structures determined by weak
forces.
8. Primary structure
• Refers-Sequence of amino acids present in
polypeptide chain . These are formed by
assembly joined with help of covalent bonds
or peptide bonds.
• Secondary Structure-
• Local regularly occurring structure in proteins
formed due to hydrogen bonds between
backbone atoms.
• Examples-1)Alpha helix
2)Beta sheets
9. Alpha helix
• Right handed spiral structure.
• Side chain extends outwards.
• Pitch-5.4 A; length-12 residues (approx);helical turns-
3(approx).
• Stabilized by hydrogen bonding that are arranged such that
peptide carbonyl oxygen and amide hydrogen.
11. Beta pleated sheet
• Formed when 2 or more polypeptides line up side by side.
• Individual polypeptide-beta strand.
• Each beta strand is fully extended.
• They are stabilized by hydrogen bond between N-H and
carbonyl groups of adjacent cells.
12.
13. • Beta pleated sheets are of two types-
• A)Anti-parallel beta sheet- Neighbouring hydrogen bonded
polypeptide chain run in opposite direction.
• B)Parallel beta sheet-Hydrogen bonded chains extended in
same direction.
15. • Two major sorts of connection between beta strands-
• 1)Hairpin or same end connection
• 2)Cross over or opposite end connection.
16.
17. Tertiary Structures
• Defines overall 3-D shape of protein.
• Tertiary structure is based on various types of
interactions between side chains of
polypeptide chain.
• Example-1)Globular proteins
2) Fibrous proteins
18. Quaternary structures
Involves clustering of several individual peptide or protein chains
into specific shape.
Two types-1) Homodimer -Association between identical
polypeptide chains.
2) Heterodimer-Interaction between subunits of very different
structures.
19.
20. Protein Folding
• Peptide bond allows for rotation around it & therefore protein
can fold and orient R groups in favourable positions.
• Turns and loops
• Loops and turns connect alpha and beta helices.
• Loops have only 4-5 amino acid residues called turns when
have internal hydrogen bonds.
22. amino (N) terminal end
carboxy (C) terminal end
C
i
Ri-1
H
C
i+1
Ni+1
C'i
Ci
Ni
C'i-1
Ri+1
H
Oi
Oi-1
Hi+1
Hi
C
i-1
H
i
i
peptide planes
--> Ni-C- C’i -Ni+1
--> C’i-1-Ni-C- C’i
Notice that these are defined
from N to C terminus, using
main chain atoms only.
A residue’s conformation is usually
listed as (,), since w is close
to 180 for almost all residues.
Torsional angles are defined by
four atoms:
and angles
23. ● The two torsion angles of the polypeptide
chain, also called Ramachandran angles, describe
the rotations of the polypeptide backbone around
the bonds between – N-Cα (called Phi, φ) and –
Cα-C (called Psi, ψ).
● The Ramachandran plot provides an easy way
to view the distribution of torsion angles of a
protein structure
and angles
24. and angles
● It also provides an overview of allowed and
disallowed regions of torsion angle values,
serving as an important indicator of the quality
of protein three-dimensional structures.
25. and angles
● Torsion angles are among the most important local
structural parameters that control protein folding
● Essentially, if we would have a way to predict the
Ramachandran angles for a particular protein, we
would be able to predict its 3D folding.
● The reason is that these angles provide the
flexibility required for the polypeptide backbone to
adopt a certain fold,
● Since the third possible torsion angle within the
protein backbone (called omega, ω) is essentially flat
and fixed to 180 degrees
26. -180 0 180
0
180
-180
allowed
not allowed
between R groups
and between carbonyls
or combinations of
an R group, carbonyl
or amide group.
27. from web version of JS Richardson’s “Anatomy and
Taxonomy of Protein Structure”
http://kinemage.biochem.duke.edu/~jsr/index.html
● Theoretical calculations using
hard sphere approximations
suggest which phi and psi
combinations cause clashes, and
between which atoms.
● Cross-hatched regions are
“allowed”
for all residue types. The larger
regions in the four corners are
allowed for glycine because it
lacks a side chain, so that no
steric clashes involving the beta
carbon are possible.
STERIC CLASHES DISALLOW SOME F
AND COMBINATIONS
28. OBSERVED F AND COMBINATIONS
IN PROTEINS
Phi-psi combinations actually
observed in proteins with known
high-quality structures.
Gly residues are excluded from
this plot, as are Pro residues and
residues which precede Pro
(more on this later).
Contours enclose 98% and 99.95%
of the data respectively.
Notice that the observed conformations
do not exactly coincide with the
theoretically allowed/disallowed confs
based on steric clashes.
from Lovell SC et al.
Proteins 50, 437 (2003)
29. SAMPLE “RAMACHANDRAN PLOT”
FOR A PROTEIN
red= allowed
yellow= additionally allowed
pale yellow= generously allowed
white= disallowed
● This protein has 219 residues,
90% of which are in the “allowed”
region and 10% of which are
in “additionally allowed” regions.
None are in the other regions
(except glycines,
which don’t count)
● The squares denote non-glycine
residues, while the triangles are
glycines. Glycines have no side
chain and are not as restricted
because of the lack of side chain
steric clashes.
30. THE RAMACHANDRAN PLOT
• The two torsion angles of the
polypeptide chain, describe the
rotations of the polypeptide
backbone around the bonds
between N-Cα (called Phi, φ) and
Cα-C (called Psi, ψ)
• It provides an easy way to view the
distribution of torsion angles of a
protein structure
31. THE RAMACHANDRAN PLOT
• It also provides an overview of allowed
and disallowed regions of torsion angle
values
– serve as an important indicator of the
quality of protein three-dimensional
structures
• Torsion angles are among the most
important local structural parameters that
control protein folding
• Third possible torsion angle within the
protein backbone (called omega, ω)
32. THE RAMACHANDRAN PLOT
• If we would have a way to predict the Ramachandran angles for a particular
protein, we would be able to predict its 3D folding
• The reason is that these angles provide the flexibility required for the
polypeptide backbone to adopt a certain fold, since ω is essentially flat and fixed
to 180 degrees
– This is due to the partial double-bond character of the peptide bond, which
– restricts rotation around the C-N bond, placing two successive alpha-
carbons and C, O, N and H between them in one plane
– Thus, rotation of the protein chain can be described as rotation of the
peptide bond planes relative to each other
33. TORSION ANGLES
• Torsion angles are dihedral
angles, which are defined by
4 points in space
• In proteins the two torsion
angles phi and psi describe the
rotation of the polypeptide
chain around the two bonds on
both sides of the C alpha atom
34. DIHEDRAL ANGLE
• The standard IUPAC definition of a dihedral
angle is illustrated in the figure below
• A, B, C and D illustrate the position of the 4
atoms used to define the dihedral angle
• The rotation takes place around the central B-
C bond • The view on the right is along the B-C
bond with atom A placed at 12 o'clock
• The rotation around the B-C bond is described
by the A-B-D angle shown of the right figure:
Positive angles correspond to clockwise rotation
35. PROTEIN BACKBONE
• The protein backbone can be described in
terms of the phi, psi and omega torsion
angles of the bonds: The phi angle is the
angle around the -N-CA- bond (where 'CA'
is the alpha-carbon)
• The psi angle is the angle around the -CA-C-
bond.
• The omega angle is the angle around the -
C-Nbond (i.e. the peptide bond)
36. THE RAMACHANDRAN PLOT
• In a polypeptide the main chain N-Calpha and Calpha-C
bonds relatively are free to rotate. These rotations are
represented by the torsion angles phi and psi,
respectively
• G N Ramachandran used computer models of small
polypeptides to systematically vary phi and psi with the
objective of finding stable conformations
• For each conformation, the structure was examined for
close contacts between atoms
• Atoms were treated as hard spheres with dimensions
corresponding to their van der Waals radii
• Therefore, phi and psi angles which cause spheres to
collide correspond to sterically disallowed conformations of
the polypeptide backbone
37. THE RAMACHANDRAN PLOT
• In the diagram the white areas correspond to conformations
where atoms in the polypeptide come closer than the sum of
their van der Waals radii.
• These regions are sterically disallowed for all amino acids
except glycine which is unique in that it lacks a side chain
38. THE RAMACHANDRAN PLOT
The red regions correspond to conformations where there are no
steric clashes, ie these are the allowed regions namely the alpha-
helical and beta-sheet conformations
• The yellow areas show the allowed regions if slightly shorter van
der Waals radi are used in the calculation, ie the atoms are allowed
to come a little closer together
• This brings out an additional region which corresponds to the left-
handed alpha-helix
40. THE RAMACHANDRAN PLOT
• L-amino acids cannot form extended regions of lefthanded helix –
but occassionally individual residues adopt this conformation
– These residues are usually glycine but can also be asparagine or
aspartate where the side chain forms a hydrogen bond with the
main chain and therefore stabilises this otherwise unfavourable
conformation
– The 3(10) helix occurs close to the upper right of the alpha-
helical region and is on the edge of allowed region indicating lower
stability
41. 310 HELIX
• A 310 helix is a type of secondary structure
• found (often) in proteins and polypeptides
• Top view of the same helix shown to the right
• Three carbonyl groups are pointing upwards towards the viewer
– spaced roughly 120° apart on the circle
– corresponding to 3.0 amino-acid residues per turn of the helix
42. THE RAMACHANDRAN PLOT
• Disallowed regions generally involve steric hindrance
between the side chain C-beta methylene group and main
chain atoms
• Glycine has no side chain and therefore can adopt phi and
psi angles in all four quadrants of the Ramachandran plot
• Hence it frequently occurs in turn regions of proteins
where any other residue would be sterically hindered
43. SIGNIFICANCE OF RAMACHANDRAN PLOT
• Ramachandran plots show the relationship between the phi and psi angles of a
protein referring to dihedral angles between the N and the C-alpha and the C-
alpha and the C-beta. As an aside, the omega angle between the C-beta and the N
tends to be fixed due to pi-pi interactions.
• There are limits to possible distributions of phi and psi angles due to steric clashes
between the side chains. Furthermore other limitations from higher order
structure will result in the adoption of defined phi-psi angles. Using data from
solved crystal structures, it can be seen that the dihedral angles will adopt specific
conformations in a protein.
44. • Furthermore, it can be noted that some of these conformations relate to
specific secondary structures. As seen above, peptides in alpha-helices and
beta-sheets adopt a even more limited set of phi-psi angles. Certain amino
acids like glycine and proline, which differ from from canonical amino acids
have an unique Ramachandran plot.
• The angles from a Ramachandran plot are useful not only for determining a
amino acids' role in secondary structure but can also be used to verify the
solution to a crystal structure. Furthermore, it assists with constraining
structure prediction simulations and helps with defining energy functions