This document discusses protein function and regulation. It covers how proteins bind specifically to molecules through noncovalent bonds in a binding site [1]. Enzymes function as catalysts by lowering activation energy for reactions and binding unstable transition states [2]. Protein activity is regulated by mechanisms like feedback inhibition, allosteric regulation, phosphorylation, and scaffolding [3]. Common methods to analyze proteins include yeast two-hybrid, bioinformatics, affinity tags, proteomics, and mass spectrometry.
A genome is an organism’s complete set of DNA or complete genetic makeup, The entire DNA complement. It describes the identity and the sequence of genes of an organism.
Genomics is the study of entire genomes(structure, function, evolution, mapping, and editing of genomes)
Executing the sequencing and analysis of entire human genome enables more rapid and effective identification of disease associated genes and provide drug companies with pre validated targets.
Proteomics is the systematic high-throughput separation and characterization of proteins within biological systems./ large scale study of protein and their functions.
Proteomics measures protein expression directly, not via gene expression, thus achieving better accuracy. Current work uses 2-dimensional polyacrylamide gel electrophoresis(2D- PAGE) and mass spectrometry.
New separation and characterization technologies, such as protein microarray and high throughput chromatography are being developed.
A genome is an organism’s complete set of DNA or complete genetic makeup, The entire DNA complement. It describes the identity and the sequence of genes of an organism.
Genomics is the study of entire genomes(structure, function, evolution, mapping, and editing of genomes)
Executing the sequencing and analysis of entire human genome enables more rapid and effective identification of disease associated genes and provide drug companies with pre validated targets.
Proteomics is the systematic high-throughput separation and characterization of proteins within biological systems./ large scale study of protein and their functions.
Proteomics measures protein expression directly, not via gene expression, thus achieving better accuracy. Current work uses 2-dimensional polyacrylamide gel electrophoresis(2D- PAGE) and mass spectrometry.
New separation and characterization technologies, such as protein microarray and high throughput chromatography are being developed.
Introduction to proteomics, techniques to study proteomics such as protein electrophoresis, chromatography and mass spectrometry and protein database analysis, case studies derived from scientific literature including comparisons between healthy and diseased tissues, new approaches to analyse metabolic pathways, comprehensive analysis of protein-protein interactions in different cell types.
Proteomics and its applications in phytopathologyAbhijeet Kashyap
Dear friends, I Abhijeet kashyap presenting the basics of proteomics to you all . Proteomics is the large-scale study of proteins, particularly their structures and functions.Proteomics helps in understanding the structure and function of different proteins as well as protein-protein interactions of an organism.
Introduction: Enzyme definition, Composition: Protein part Apoprotein)/Non-protein(cofactors/coenzymes)
Applications, Enzyme Nomenclature
Basic Structure of Enzyme
Homo-multimers
Hetero-multimers
Multiple Forms of Enzymes
Origins of Enzyme Variants: Genetic and Non-genetic
Example of Genetic and Non-genetic
Iso-enzymes: Examples
Specificity of Enzymes
protein targeted chimerase(protac) in pharmaceutical chemistryIndraKumar93
overview on protein targerted chimerase (protac) in recent development and it is a good bindind affinity for attaches to the microorganism and destroy it. It is in the phase 2 clinical trials and not yet to market. only few industries are sucessfully conducting phase 2 clinical trials.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Introduction to proteomics, techniques to study proteomics such as protein electrophoresis, chromatography and mass spectrometry and protein database analysis, case studies derived from scientific literature including comparisons between healthy and diseased tissues, new approaches to analyse metabolic pathways, comprehensive analysis of protein-protein interactions in different cell types.
Proteomics and its applications in phytopathologyAbhijeet Kashyap
Dear friends, I Abhijeet kashyap presenting the basics of proteomics to you all . Proteomics is the large-scale study of proteins, particularly their structures and functions.Proteomics helps in understanding the structure and function of different proteins as well as protein-protein interactions of an organism.
Introduction: Enzyme definition, Composition: Protein part Apoprotein)/Non-protein(cofactors/coenzymes)
Applications, Enzyme Nomenclature
Basic Structure of Enzyme
Homo-multimers
Hetero-multimers
Multiple Forms of Enzymes
Origins of Enzyme Variants: Genetic and Non-genetic
Example of Genetic and Non-genetic
Iso-enzymes: Examples
Specificity of Enzymes
protein targeted chimerase(protac) in pharmaceutical chemistryIndraKumar93
overview on protein targerted chimerase (protac) in recent development and it is a good bindind affinity for attaches to the microorganism and destroy it. It is in the phase 2 clinical trials and not yet to market. only few industries are sucessfully conducting phase 2 clinical trials.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
2. PROTEIN
FUNCTION
MODULE 1: LESSON 2 OF 3
BIOL6299 Fall 2022
Northeastern University
(Source: Bruce Alberts; Alexander Johnson; Julian Lewis; David Morgan; Martin Raff; Keith Roberts; Peter Walter: 6th Edition)
3. INTRODUCTION
• In this lesson, we discuss how proteins bind to specific molecules and how their
activity determined protein function in the cell.
• By the end of this lesson, you will have the opportunity to:
• Explain the various types of protein binding.
• Discuss how enzymes are regulated within the cells
• Describe major protein mechanisms and modifications that have major impacts in cell
signaling and regulation.
• Identify common methods used to analyze proteins and their cellular roles.
4. MODULE 1
LESSON 2
OF 3
•Protein Specificity
•Binding site of Proteins
•Types of protein binding
•Role of enzymes
Protein binding and the role of Enzymes
•Feedback inhibition
•Allosteric Regulation
•Protein modifications and their role in protein regulation
Protein Regulation
•Yeast two hybrid, Bioinformatics, Affinity Tags, Proteomics,
Protein Mass Spectrometry
Methods to Analyze Proteins
6. PROTEIN SPECIFICITY
Ø Ligand – molecule bound by
a protein, the binding site of
which is often located in the
cavity of the protein.
Ø Selectivity and affinity is
dependent upon the
noncovalent bonds.
7. THE BINDING SITE OF A PROTEIN
Ø The folding of the polypeptide chain creates
a cavity on the protein surface.
Ø This cavity consists of a set of amino acid
side chains arranged to form noncovalent
bonds only with certain ligands.
9. PROTEIN-LIGAND
INTERACTION -
ANTIBODIES
• Antibodies are proteins generated in response
to foreign invaders.
• To be effective, each Ab must bind tightly to a
specific antigen, tagging it for destruction by
other immune cells.
10. THE ROLE OF
ENZYMES
• Enzymes are proteins that bind substrates and
convert them into other chemicals called
products.
• Enzymes have higher affinity for unstable
transition states of substrate than for stable
form.
• Enzymes reduce the activation energy and act
as catalysts to speed up reactions.
12. CATALYSIS BY LYSOZYMES
Ø LYSOZYME REACTION INVOLVES HYDROLYSIS.
Ø LYSOZYMES CATALYZES THE CLEAVAGE OF SPECIFIC COVALENT BOND IN THE POLYSACCHARIDE BACKBONE CHAIN AND
SEVERS THE CHAIN.
14. PROTEIN REGULATION – FEEDBACK
INHIBITION
• Enzyme activity is regulated by 4 distinct mechanisms-
• Controlling the level of gene expression of each enzyme.
• Confining sets of enzymes to particular subcellular compartments.
• Covalent modifications of the protein itself.
• Regulation by a molecule other than the substrate.
• Feedback inhibition-
• Involves substrate binding to the enzyme at a special regulatory site outside the active site,
thereby altering the rate by which the enzyme converts substrate to products.
15. FEEDBACK
INHIBITION
Positive feedback – stimulates
enzyme activity
Negative feedback – inhibits
enzyme activity (mostly of an
enzyme that acts earlier in the
pathway)
20. KINASES – CYCLIN
DEPENDENT
KINASES
• CDKs are serine and
threonine kinases
• Required for normal cell-
cycle control.
• There are 3 signals/inputs
required for fully functional
Cdk.
21. KINASES – SRC KINASES
Src protein is a tyrosine kinase.
Through tyrosine phosphorylation, they transmit intracellular signals from the receptor itself.
It has 3 main domains on the Src protein:
2 peptide binding molecules- SH3 and SH2
1 catalytic kinase domain- SH1
22. KINASES – SRC KINASES CONTD…
Two signals are required to activate Src kinase:
24. GTPASE – MOLECULAR SWITCHES
* Phosphorylation can also regulate proteins as part of the guanine nucleotide GTP,
which also binds tightly to the protein.
25. THE SCAFFOLDING
PROTEINS: SCF
UBIQUITIN LIGASE
*Proteins can also form complexes that serve as large
protein machines.
E.g.: SCF ubiquitin ligase (has 5 subunits) binds
different target proteins and covalently attaches a
ubiquitin polypeptide, which tags the protein for
destruction.
27. PROTEIN MODIFICATIONS: P53
Ø Combinatorial Regulatory role: Proteins can be modified at multiple amino acids.
Ø E.g.: p53 (tumor suppressor gene – apoptosis, cell cycle and damage response).
Ø P53 can be regulated by many different combinations of PTMs at 20 different sites.
28. METHODS TO ANALYZE
PROTEINS
BIOL6299 Spring 2022
Northeastern University
• YEAST TWO HYBRI D
• BI OI NFORMATI CS
• AFFI NI TY TAGS
• PROTEOMI CS
• PROTEI N MASS SPECTROMETRY
30. BIOINFORMATICS
• Uses many areas of computer science,
mathematics and engineering to process
biological data, to develop software tools to
generate useful biological knowledge.
31. AFFINITY TAGS
• Affinity tags are appended to proteins so that
they can be purified from their crude biological
source using an affinity technique.
• Tags: His, GFP, Myc, etc.
• These tags are useful for immunoblotting,
immunofluorescence and immunoprecipitation
experiments.
32. PROTEOMICS
• Proteomics is a large scale study of proteins, particularly
their structure and function.
• Proteome is the entire compliment of proteins, including
modifications made to a particular set of proteins,
produced by an organism or system (varies with time and
distinct requirements or stresses, that a cell or organism
undergoes).
33. PROTEIN MASS
SPECTROMETRY
• Important for characterization of proteins.
• 2 primary methods used for ionization of whole proteins
are:
• Electrospray ionization (ESI)
• Matrix assisted laser desorption/ionization (MALDI)
34. IN THIS LESSON:
• Learned about the various types of protein binding
• Discussed how enzymes are regulated within the cells.
• Described major protein mechanisms and modifications that have major impacts
in cell signaling and regulation.
• Identified common methods used to analyze proteins and their cellular roles.