This document discusses the different levels of protein structure: primary, secondary, tertiary, and quaternary. The primary structure refers to the amino acid sequence. Secondary structure includes alpha helices, beta sheets, and beta turns formed by hydrogen bonding between amino acids. Tertiary structure is the 3D conformation determined by interactions between side chains. Quaternary structure refers to the arrangement of multiple polypeptide subunits in multimeric proteins. The structures are determined through techniques like X-ray crystallography and NMR.
Proteins are the macromolecules responsible for the biological processes in the cell. They consist at their most basic level of a chain of amino acids, determined by the sequence of nucleotides in a gene. Depending on the amino acid sequence (different amino acids have different biochemical properties) and interactions with their environment, proteins fold into a three-dimensional structure, which allows them to interact with other proteins and molecules and perform their function
Proteins are the macromolecules responsible for the biological processes in the cell. They consist at their most basic level of a chain of amino acids, determined by the sequence of nucleotides in a gene. Depending on the amino acid sequence (different amino acids have different biochemical properties) and interactions with their environment, proteins fold into a three-dimensional structure, which allows them to interact with other proteins and molecules and perform their function
RNA- A polymer of ribonucleotides, is a single stranded structure. There are three major types of RNA- m RNA,t RNA and r RNA. Besides that there are small nuclear,micro RNAs, small interfering and heterogeneous RNAs. Each of them has a specific structure and performs a specific function.
Enzyme inhibition is explained with its kinetics, animations showing mechanism of inhibitors action, examples of inhibitors are explained in detail with Enzyme inhibited.
by Dr. N. Sivaranjani, MD
An enzyme is a substance that acts as a catalyst in living organisms, regulating the rate at which chemical reactions proceed without itself being altered in the process. The biological processes that occur within all living organisms are chemical reactions, and most are regulated by enzymes
Amino acids are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (Ī±-), beta- (Ī²-), gamma- (Ī³-) or delta- (Ī“-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues.Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
Enzymes definitions, types & classificationJasmineJuliet
Ā
Enzyme - Introduction, Biocatalysts, Definition of enzymes, Types of enzymes, classification of enzyme, Nomenclature of enzymes, EC number, Types of enzymes with examples, and reaction.
RNA- A polymer of ribonucleotides, is a single stranded structure. There are three major types of RNA- m RNA,t RNA and r RNA. Besides that there are small nuclear,micro RNAs, small interfering and heterogeneous RNAs. Each of them has a specific structure and performs a specific function.
Enzyme inhibition is explained with its kinetics, animations showing mechanism of inhibitors action, examples of inhibitors are explained in detail with Enzyme inhibited.
by Dr. N. Sivaranjani, MD
An enzyme is a substance that acts as a catalyst in living organisms, regulating the rate at which chemical reactions proceed without itself being altered in the process. The biological processes that occur within all living organisms are chemical reactions, and most are regulated by enzymes
Amino acids are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (Ī±-), beta- (Ī²-), gamma- (Ī³-) or delta- (Ī“-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues.Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
Enzymes definitions, types & classificationJasmineJuliet
Ā
Enzyme - Introduction, Biocatalysts, Definition of enzymes, Types of enzymes, classification of enzyme, Nomenclature of enzymes, EC number, Types of enzymes with examples, and reaction.
Secondary Structure Prediction of proteins Vijay Hemmadi
Ā
Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
Some good references on the subject:
Domains were added to Node.js in 0.8, but their use and workings have been a relative mystery. In short, domains are a structured way of reacting to uncaught exceptions; for example, when creating an HTTP server, you can use domains to send 500 errors when exceptions occur instead of crashing your server. This talk will go over what domains are, how to use them, and some of the subtleties behind how they work.
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
Amino acisd structure
Peptide bond formation
Analysis of protein Structure- X-ray Crystallography
Different structural levels of proteins with examples.
Importance of protein structure
Creutzfeldt-Jacob-Disease due to changes in normal protein conformation.
In this pdf amino acid and protein classification is given in excellent manner.
Amino acids are molecules that combine to form proteins. Amino acids and proteins are the building blocks of life.When proteins are digested or broken down, amino acids are left. The human body uses amino acids to make proteins to help the body:Break down food,Grow,Repair body tissue,Perform many other body functions.Amino acids can also be used as a source of energy by the body.
Amino acids are classified into three groups:
Essential amino acids
Nonessential amino acids....
Function and Classification of protein given in this pdf .
Structure of proteins given in this pdf with different types of interaction between amino acids like hydrogen bonding , intermolecular and intramolecular bondings. Also structure of protein given in primary, secondary, tertiary and quarternary forms.
Physicochemical properties of protein also given in this pdf.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Ā
Are you looking to streamline your workflows and boost your projectsā efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, youāre in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part āEssentials of Automationā series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Hereās what youāll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
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Weāll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Donāt miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
"Impact of front-end architecture on development cost", Viktor TurskyiFwdays
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I have heard many times that architecture is not important for the front-end. Also, many times I have seen how developers implement features on the front-end just following the standard rules for a framework and think that this is enough to successfully launch the project, and then the project fails. How to prevent this and what approach to choose? I have launched dozens of complex projects and during the talk we will analyze which approaches have worked for me and which have not.
Search and Society: Reimagining Information Access for Radical FuturesBhaskar Mitra
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The field of Information retrieval (IR) is currently undergoing a transformative shift, at least partly due to the emerging applications of generative AI to information access. In this talk, we will deliberate on the sociotechnical implications of generative AI for information access. We will argue that there is both a critical necessity and an exciting opportunity for the IR community to re-center our research agendas on societal needs while dismantling the artificial separation between the work on fairness, accountability, transparency, and ethics in IR and the rest of IR research. Instead of adopting a reactionary strategy of trying to mitigate potential social harms from emerging technologies, the community should aim to proactively set the research agenda for the kinds of systems we should build inspired by diverse explicitly stated sociotechnical imaginaries. The sociotechnical imaginaries that underpin the design and development of information access technologies needs to be explicitly articulated, and we need to develop theories of change in context of these diverse perspectives. Our guiding future imaginaries must be informed by other academic fields, such as democratic theory and critical theory, and should be co-developed with social science scholars, legal scholars, civil rights and social justice activists, and artists, among others.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
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Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
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The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
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Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
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The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. Whatās changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
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In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
ā¢ The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
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ā¢ Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
ā¢ Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
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Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
2. ā¢ Proteins are an important class of
biological macromolecules
which are the polymers of amino
acids.
ā¢ Biochemists have distinguished
several levels of structural
organization of proteins. They
are:
ā Primary structure
ā Secondary structure
ā Tertiary structure
ā Quaternary structure
INTRODUCTION
3. PRIMARY STRUCTURE
ā¢ The primary structure of protein refers to the sequence of amino
acids present in the polypeptide chain.
ā¢ Amino acids are covalently linked by peptide bonds.
ā¢ Each component amino acid in a polypeptide is called a āresidueā or
āmoietyā
ā¢ By convention, the 10 structure of a protein starts from the amino-
terminal (N) end and ends in the carboxyl-terminal (C) end.
4. IMPORTANCE OF PRIMARY STRUCTURE
ā¢ To predict 20 and 30 structures from sequence homologies with
related proteins. (Structure prediction)
ā¢ Many genetic diseases result from abnormal amino acid sequences.
ā¢ To understand the molecular mechanism of action of proteins.
ā¢ To trace evolutionary paths.
ā¢ End group analysis ā Edman degradation.
ā¢ Gene sequencing method.
METHODS OF AMINO ACID SEQUENCE DETERMINATION
5. SECONDARY STRUCTURE
ā¢ Localized arrangement of adjacent amino acids formed as the polypeptide
chain folds.
ā¢ It consists of
ā¢ Linus Pauling proposed some essential features of peptide units and
polypeptide backbone. They are:
ā The amide group is rigid and planar as a result of resonance. So rotation
about C-N bond is not feasible.
ā Rotation can take place only about N- CĪ± and CĪ± ā C bonds.
ā Trans configuration is more stable than cis for R grps at CĪ±
ā¢ From these conclusions Pauling postulated 2 ordered structures Ī± helix and
Ī² sheet
Ī±-helix
Ī²-pleated sheet
Ī²-bends
Non repetitive structures
Super secondary structures
6. POLYPEPTIDE
CHAIN CONFORMATIONS
ā¢ The only reasonably free movements
are rotations around the C Ī±-N bond
(measured as Ļ ) and the C Ī±-C bond
(measured as Ń°).
ā¢ The conformation of the backbone
can therefore be described by the
torsion angles (also called dihedral
angles or rotation angles)
9. ā¢ White regions : Sterically
disallowed for all amino acids
except glycine.
ā¢ Red regions : allowed regions
namely the a-helical and b-sheet
conformations.
ā¢ Yellow areas : outer limit
A Ramachandran plot (also known as a Ramachandran diagram or
a [Ļ,Ļ] plot), originally developed in 1963 by G. N. Ramachandran.
RAMACHANDRAN PLOT
10. ā¢ Spiral structure
ā¢ Tightly packed, coiled polypeptide
backbone core.
ā¢ Side chain extend outwards
ā¢ Stabilized by H bonding b/w
carbonyl oxygen and amide
hydrogen.
ā¢ Amino acids per turn ā 3.6
ā¢ Pitch is 5.4 A
ā¢ Alpha helical segments are found in
many globular proteins like
myoglobins, troponin- C etc.
ALPHA HELIX
H bonding
11. ā¢ Formed when 2 or more polypeptides
line up side by side.
ā¢ Individual polypeptide - Ī² strand
ā¢ Each Ī² strand is fully extended.
ā¢ They are stabilized by H bond b/w N-H
and carbonyl grps of adjacent chains.
BETA PLEATED SHEET
2 types
Parallel Anti -Parallel
N C N
N NC
C
C
14. BETA BENDS
ā¢ Permits the change of direction of the
peptide chain to get a folded structure.
ā¢ It gives a protein globularity rather than
linearity.
ā¢ H bond stabilizes the beta bend
structure.
ā¢ Proline and Glycine are frequently
found in beta turns.
ā¢ Beta turns often promote the formation
of antiparallel beta sheets.
ā¢ Occur at protein surfaces.
ā¢ Involve four successive aminoacid
residues
16. SUPER SECONDARY STRUCTURES
(MOTIFS)
Beta barrelĪ²-meander motif
beta-alpha-beta motif Greek key motif
Certain groupings of secondary structural elements are
called motifs.
17. TERTIARY STRUCTURE
ā¢ Tertiary structure is the three-
dimensional conformation of a
polypeptide.
ā¢ The common features of protein
tertiary structure reveal much about
the biological functions of the proteins
and their evolutionary origins.
ā¢ The function of a protein depends on
its tertiary structure. If this is disrupted,
it loses its activity.
18. DOMAINS
ā¢ Polypeptide chains containing more than ,200 residues usually
fold into two or more globular clusters known as domains.
ā¢ Fundamental functional and 3 dimensional structure of
proteins.
ā¢ Domains often have a specific function such as the binding of
a small molecule.
ā¢ Many domains are structurally independent units that have the
characteristics of small globular proteins.
The two-domain protein glyceraldehyde-
3-phosphate dehydrogenase.
NAD+
19. INTERACTIONS STABILIZING 30
STRUCTURE
ā¢ This final shape is
determined by a variety of
bonding interactions
between the "side chains"
on the amino acids.
ā¢ Hydrogen bonds
ā¢ Ionic Bonds
ā¢ Disulphide Bridges
ā¢ Hydrophobic Interactions:
21. DETERMINATION OF TERTIARY
STRUCTURE
ā¢ The known protein structures have come to light through:
ā¢ X-ray crystallographic studies
ā¢ Nuclear Magnetic Resonance studies
ā¢ The atomic coordinates of most of these structures are
deposited in a database known as the Protein Data Bank
(PDB).
ā¢ It allows the tertiary structures of a variety of proteins to be
analyzed and compared.
22. ā¢ The biological function of some
molecules is determined by multiple
polypeptide chains ā
multimeric proteins.
ā¢ Arrangement of polypeptide sub unit
is called quaternary structure.
ā¢ Sub units are held together by non
covalent interactions.
ā¢ Eg: Hemoglobin has the subunit
composition a2b2
QUATERNARY STRUCTURE
Quaternary structure of hemoglobin.
23. RECENT DEVELOPMENTS
ā¢ A team of scientists at The Scripps Research Institute and the
National Institutes of Health (NIH) has discovered the
structure of a protein ā dynamin, that pinches off tiny pouches
from cellās outer membranes.
ā¢ Scientists at the Institute of Structural and Molecular Biology
have revealed the structure of a complex protein called FimD
that acts as an assembly platform for the pili of cystitis
bacteria.
ā¢ Researchers from the Walter and Eliza Hall Institute have
found a structural surprise in a type of protein, Bcl-w ,that
encourages cell survival, raising interesting questions about
how the proteins function to influence programmed cell death.
24. CONCLUSION
ā¢ Proteins are extraordinarily complex molecules. Of all the
molecules encountered in living organisms, proteins have the
most diverse functions.
ā¢ So a basic understanding of the structure of proteins is
necessary to comprehend its role in organisms.
ā¢ Further researches will provide more insight into the structure
of several other proteins in the coming year.
25. REFERENCE
ā¢ Voet, Donald; Voet Judith. Biochemistry, 3rd edition, John
Wiley and sons.
ā¢ Champe, Pamela.C, Harvey, Richard A, Ferrier Denise R
(2005). Lippincottās Illustrated Reviews: Biochemistry, 3rd
edition. Lippincott William and Wilkins.
ā¢ McKee Trudy, McKee James R (2003), Biochemistry: The
molecular basis of life, 3rd edition, McGraw Hill.
ā¢ http://esciencenews.com/articles/2011/06/01/new.antibiotics.a.
step.closer.with.discovery.bacterial.protein.structure
ā¢ http://www.eurekalert.org/pub_releases/2010-04/sri-
srs042610.php
ā¢ http://www.physorg.com/news/2011-10-cell-survival-protein-
reveals.html