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
Enzymes definitions, types & classificationJasmineJuliet
Enzyme - Introduction, Biocatalysts, Definition of enzymes, Types of enzymes, classification of enzyme, Nomenclature of enzymes, EC number, Types of enzymes with examples, and reaction.
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
Enzymes definitions, types & classificationJasmineJuliet
Enzyme - Introduction, Biocatalysts, Definition of enzymes, Types of enzymes, classification of enzyme, Nomenclature of enzymes, EC number, Types of enzymes with examples, and reaction.
Active sites of the enzyme is that point where substrate molecule bind for the chemical reaction. It is generally found on the surface of enzyme and in some enzyme it is a “Pit” like structure
The active site is a three-dimensional cleft formed by groups that come from different parts of the amino acid sequence
The active site takes up a relatively small part of the total volume of an enzyme
Active sites are clefts or crevices
Substrates are bound to enzymes by multiple weak attractions.
The specificity of binding depends on the precisely defined arrangement of atoms in an active site.
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.
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.
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
Primary structure of protein
Secondary structure of protein
Tertiary structure of protein
Quaternary structure of protein
Methods to determine protein structure
Conclusion
References
METHODS TO DETERMINE PROTEIN STRUCTURE
Each protein has a unique sequence of amino acids.
The amino acids are held together in a protein by
covalent peptide bonds or linkages.
A peptide bond are formed when amino group of an
amino acid combines with the carboxyl group of another.
The conformation of polypeptide chain by twisting or folding is referred to as secondary structure.
Two types of secondary structures α-helix and β-sheet are mainly identified.
α-Helical structure was proposed by Pauling and Corey in 1951.
It occurs when the sequence of amino acids are linked by hydrogen bonds.
Each turn of α-helix contains 3.6 amino acids.
β-pleated sheets are composed of two or more segments of fully extended peptide chains.
β-Sheets may be arranged either in parallel or anti-parallel direction.
Many globular proteins contain combinations of α-helix and β-pleated sheet secondary structure, these patterns are called supersecondary structures also called motifs.
The three dimensional arrangement of protein structure is referred to as tertiary structure.
It is a compact structure with hydrophobic side chains held interior while the hydrophilic groups are on the surface.
This type of arrangement provide stability of the molecule.
Besides the H-bongs, disulfide bonds, ionic interactions, hydrophobic interactions also contribute to the tertiary structure.
Active sites of the enzyme is that point where substrate molecule bind for the chemical reaction. It is generally found on the surface of enzyme and in some enzyme it is a “Pit” like structure
The active site is a three-dimensional cleft formed by groups that come from different parts of the amino acid sequence
The active site takes up a relatively small part of the total volume of an enzyme
Active sites are clefts or crevices
Substrates are bound to enzymes by multiple weak attractions.
The specificity of binding depends on the precisely defined arrangement of atoms in an active site.
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.
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.
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
Primary structure of protein
Secondary structure of protein
Tertiary structure of protein
Quaternary structure of protein
Methods to determine protein structure
Conclusion
References
METHODS TO DETERMINE PROTEIN STRUCTURE
Each protein has a unique sequence of amino acids.
The amino acids are held together in a protein by
covalent peptide bonds or linkages.
A peptide bond are formed when amino group of an
amino acid combines with the carboxyl group of another.
The conformation of polypeptide chain by twisting or folding is referred to as secondary structure.
Two types of secondary structures α-helix and β-sheet are mainly identified.
α-Helical structure was proposed by Pauling and Corey in 1951.
It occurs when the sequence of amino acids are linked by hydrogen bonds.
Each turn of α-helix contains 3.6 amino acids.
β-pleated sheets are composed of two or more segments of fully extended peptide chains.
β-Sheets may be arranged either in parallel or anti-parallel direction.
Many globular proteins contain combinations of α-helix and β-pleated sheet secondary structure, these patterns are called supersecondary structures also called motifs.
The three dimensional arrangement of protein structure is referred to as tertiary structure.
It is a compact structure with hydrophobic side chains held interior while the hydrophilic groups are on the surface.
This type of arrangement provide stability of the molecule.
Besides the H-bongs, disulfide bonds, ionic interactions, hydrophobic interactions also contribute to the tertiary structure.
Secondary Structure Prediction of proteins Vijay Hemmadi
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.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
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UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
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1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
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What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
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Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
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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.
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In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
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The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
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By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
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While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
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My slides at Nordic Testing Days 6.6.2024
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Unlocking Productivity: Leveraging the Potential of Copilot in Microsoft 365, a presentation by Christoforos Vlachos, Senior Solutions Manager – Modern Workplace, Uni Systems
2. • Proteins are an important class of
biological macromolecules
which are the polymers of amino
acids.
• Biochemists have distinguished
several levels of structural
organization of proteins. They
are:
– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure
INTRODUCTION
3. PRIMARY STRUCTURE
• The primary structure of protein refers to the sequence of amino
acids present in the polypeptide chain.
• Amino acids are covalently linked by peptide bonds.
• Each component amino acid in a polypeptide is called a “residue” or
“moiety”
• 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
• To predict 20 and 30 structures from sequence homologies with
related proteins. (Structure prediction)
• Many genetic diseases result from abnormal amino acid sequences.
• To understand the molecular mechanism of action of proteins.
• To trace evolutionary paths.
• End group analysis – Edman degradation.
• Gene sequencing method.
METHODS OF AMINO ACID SEQUENCE DETERMINATION
5. SECONDARY STRUCTURE
• Localized arrangement of adjacent amino acids formed as the polypeptide
chain folds.
• It consists of
• Linus Pauling proposed some essential features of peptide units and
polypeptide backbone. They are:
– The amide group is rigid and planar as a result of resonance. So rotation
about C-N bond is not feasible.
– Rotation can take place only about N- Cα and Cα – C bonds.
– Trans configuration is more stable than cis for R grps at Cα
• From these conclusions Pauling postulated 2 ordered structures α helix and
β sheet
α-helix
β-pleated sheet
β-bends
Non repetitive structures
Super secondary structures
6. POLYPEPTIDE
CHAIN CONFORMATIONS
• The only reasonably free movements
are rotations around the C α-N bond
(measured as ϕ ) and the C α-C bond
(measured as Ѱ).
• The conformation of the backbone
can therefore be described by the
torsion angles (also called dihedral
angles or rotation angles)
9. • White regions : Sterically
disallowed for all amino acids
except glycine.
• Red regions : allowed regions
namely the a-helical and b-sheet
conformations.
• Yellow areas : outer limit
A Ramachandran plot (also known as a Ramachandran diagram or
a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran.
RAMACHANDRAN PLOT
10. • Spiral structure
• Tightly packed, coiled polypeptide
backbone core.
• Side chain extend outwards
• Stabilized by H bonding b/w
carbonyl oxygen and amide
hydrogen.
• Amino acids per turn – 3.6
• Pitch is 5.4 A
• Alpha helical segments are found in
many globular proteins like
myoglobins, troponin- C etc.
ALPHA HELIX
H bonding
11. • Formed when 2 or more polypeptides
line up side by side.
• Individual polypeptide - β strand
• Each β strand is fully extended.
• 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
• Permits the change of direction of the
peptide chain to get a folded structure.
• It gives a protein globularity rather than
linearity.
• H bond stabilizes the beta bend
structure.
• Proline and Glycine are frequently
found in beta turns.
• Beta turns often promote the formation
of antiparallel beta sheets.
• Occur at protein surfaces.
• Involve four successive aminoacid
residues
15. NON REPETITIVE STRUCTURES
• A significant portion of globular
protein’s structure may be irregular
or unique.
• They include coils and loops.
• Segments of polypeptide chains
whose successive residues do not
have similar ϕ and Ѱ values are
called coils.
• Almost all proteins with more than
60 residues contain one or more
loops of 6 to 16 residues, called Ω
loops.
Space-filling model of an Ω loop
16. SUPER SECONDARY STRUCTURES
(MOTIFS)
Beta barrelβ-meander motif
beta-alpha-beta motif Greek key motif
Certain groupings of secondary structural elements are
called motifs.
17. TERTIARY STRUCTURE
• Tertiary structure is the three-
dimensional conformation of a
polypeptide.
• The common features of protein
tertiary structure reveal much about
the biological functions of the proteins
and their evolutionary origins.
• The function of a protein depends on
its tertiary structure. If this is disrupted,
it loses its activity.
18. DOMAINS
• Polypeptide chains containing more than ,200 residues usually
fold into two or more globular clusters known as domains.
• Fundamental functional and 3 dimensional structure of
proteins.
• Domains often have a specific function such as the binding of
a small molecule.
• 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
• This final shape is
determined by a variety of
bonding interactions
between the "side chains"
on the amino acids.
• Hydrogen bonds
• Ionic Bonds
• Disulphide Bridges
• Hydrophobic Interactions:
21. DETERMINATION OF TERTIARY
STRUCTURE
• The known protein structures have come to light through:
• X-ray crystallographic studies
• Nuclear Magnetic Resonance studies
• The atomic coordinates of most of these structures are
deposited in a database known as the Protein Data Bank
(PDB).
• It allows the tertiary structures of a variety of proteins to be
analyzed and compared.
22. • The biological function of some
molecules is determined by multiple
polypeptide chains –
multimeric proteins.
• Arrangement of polypeptide sub unit
is called quaternary structure.
• Sub units are held together by non
covalent interactions.
• Eg: Hemoglobin has the subunit
composition a2b2
QUATERNARY STRUCTURE
Quaternary structure of hemoglobin.
23. RECENT DEVELOPMENTS
• A team of scientists at The Scripps Research Institute and the
National Institutes of Health (NIH) has discovered the
structure of a protein – dynamin, that pinches off tiny pouches
from cell’s outer membranes.
• 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.
• 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
• Proteins are extraordinarily complex molecules. Of all the
molecules encountered in living organisms, proteins have the
most diverse functions.
• So a basic understanding of the structure of proteins is
necessary to comprehend its role in organisms.
• Further researches will provide more insight into the structure
of several other proteins in the coming year.
25. REFERENCE
• Voet, Donald; Voet Judith. Biochemistry, 3rd edition, John
Wiley and sons.
• Champe, Pamela.C, Harvey, Richard A, Ferrier Denise R
(2005). Lippincott’s Illustrated Reviews: Biochemistry, 3rd
edition. Lippincott William and Wilkins.
• McKee Trudy, McKee James R (2003), Biochemistry: The
molecular basis of life, 3rd edition, McGraw Hill.
• http://esciencenews.com/articles/2011/06/01/new.antibiotics.a.
step.closer.with.discovery.bacterial.protein.structure
• http://www.eurekalert.org/pub_releases/2010-04/sri-
srs042610.php
• http://www.physorg.com/news/2011-10-cell-survival-protein-
reveals.html