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Protein Structure and Folding

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Protein Structure and Folding

After a polypeptide is produced in protein synthesis, it's not necessarily a functional protein yet! Explore protein folding that occurs within levels of protein structure with the Amoeba Sisters! Primary, secondary, tertiary, and quaternary protein structure levels are briefly discussed. Video also mentions chaperonins (chaperone proteins) and how proteins can be denatured.

Table of Contents:
00:00 Intro
0:41 Reminder of Protein Roles
1:06 Modifications of Proteins
1:25 Importance of Shape for Proteins
1:56 Levels of Protein Structure
2:06 Primary Structure
3:10 Secondary Structure
3:45 Tertiary Structure
4:58 Quaternary Structure [not in all proteins]
6:01 Proteins often have help in folding [introduces chaperonins]
6:40 Denaturing Proteins

*Further Reading Suggestions*

Related to Protein Misfoldings:




Learn About The Protein Folding Problem:



Factual References:

OpenStax, Biology. OpenStax CNX. Jun 1, 2018

Reece, J. B., & Campbell, N. A. (2011). Campbell biology. Boston: Benjamin Cummings / Pearson.


The Amoeba Sisters videos demystify science with humor and relevance. The videos center on Pinky's certification and experience in teaching biology at the high school level. For more information about The Amoeba Sisters, visit:


We cover the basics in biology concepts at the secondary level. If you are looking to discover more about biology and go into depth beyond these basics, our recommended reference is the FREE, peer reviewed, open source OpenStax biology textbook:

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PROTEIN FOLDING

Proteins are made up of folded polypeptide chains, which are composed of 20 different amino acids, each with different chemical properties, that are linked to each other via covalent peptide bonds. The sequence of atoms repeating to form the peptide bonds is called the polypeptide backbone. The side chain of each amino acid, which is the part that makes it different from the other 19 amino acids, can be either polar or nonpolar. The polypeptide chain can fold in many different ways, called “conformations”. Conformations are the spatial arrangement of atoms that can result from movement of atoms without breaking of bonds.
Protein structure can be described in terms of four levels of organization – primary, secondary, tertiary, and quaternary structure. The primary structure is simply the amino acid sequence of the polypeptide chain, and it is important to remember that this sequence contains all the information necessary for the higher orders of structure. The secondary structure is formed by hydrogen-bond interactions of adjacent amino acids. Large numbers of such local interactions form α-helices and β-pleated sheets. The tertiary structure is a more compact, 3-dimensional shape. Large proteins often consist of several protein domains, which are distinct structural units that fold somewhat independently from one another. Quaternary structure is found in those proteins that have 2 or more interacting polypeptide chains, which are then termed subunits.
Let’s examine these four levels of organization in more detail. The primary structure is determined by covalent bonds holding amino acids in a specific order. However, higher orders of structure are primarily dictated by non-covalent forces – ionic bonds, hydrogen bonds, van de Waals, and hydrophobic interactions. The combined strength of large numbers of noncovalent bonds in a protein’s folding pattern determines the stability of any given conformation. The final conformation of a protein is specified by its amino acid sequence and is typically the one that minimizes its free energy.
Secondary structures include α-helices and β-sheets. An α-helix occurs where a polypeptide chain coils like a spring, with one turn every 3.6 amino acids. In α-helices, the N-H of a peptide bond is hydrogen bonded to the C=O of another peptide bond which is one coil up in the helix structure. Note also that all the N-H groups point in one direction – towards the N-terminus - and all the C=O groups point in the opposite direction – towards the C-terminus – and this is what gives the polypeptide chain polarity. The C-terminus is partially positively-charged, while the N-terminus is partially negatively-charged.
β-sheets can form parallel chains, which are made from neighbouring chains running in the same direction, or antiparallel chains, which are made from a polypeptide chain that folds back and forth on itself so that nearby sections run in opposite directions. While hydrogen bonds in an α-helix are intrastrand, hydrogen bonds in β-sheets are interstrand.
Tertiary structure formation can be nucleated by the pattern of polar and nonpolar amino acids in a polypeptide chain, which plays a central role in determining the protein’s final conformation . This is because hydrophobic molecules, such as the nonpolar side chains of certain amino acids, are entropically driven together in an aqueous environment. This limits their disruption of the hydrogen bonding of surrounding water molecules. As a result, nonpolar amino acids tend to be found predominantly in the interior of proteins. Meanwhile, polar amino acids face the outside of the protein, forming hydrogen bonds with one another and the water molecules around the protein. Those polar amino acids that are on the inside of the protein bond with one another or with the polypeptide backbone.
It is thought that protein folding happens roughly along the following lines. Secondary structures form first. Hydrophobic collapse, during which non-polar amino acids aggregate, happens next. Long-range interactions between secondary structures cause further folding to occur. Throughout this process, there may be one or more intermediate states, such as what has been termed a “molten globule”.
As a final note, there are three basic classes of proteins, which are distinguished based on shape and solubility – globular, fibrous, and membrane proteins. Globular proteins are spherical in shape, with as little surface area per volume as possible. These proteins are marginally stable, and this marginal stability facilitates motion, which in turn enables function. Hydrophilic amino acids occupy this small surface area, making these proteins highly soluble in water. Fibrous amino acids are simple, linear structures which have structural roles and are insoluble. Lastly, membrane proteins are associated with cell membranes.

Cell Membrane model from
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Protein Structure - Primary, Secondary, Tertiary, & Quarternary - Biology

This biology video tutorial provides a basic introduction into the four levels of protein structure - primary, secondary, tertiary and quarternary structure. The primary structure of a protein is based on the sequence of amino acids. The secondary structure is based on localized shapes such as the alpha helix or the beta pleated sheet. The tertiary structure of a protein describes its three-dimensional folding pattern. A tertiary structure contains one individual subunit where as a quarternary structure has multiple subunits.

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Four levels of protein structure | Chemical processes | MCAT | Khan Academy

The four levels of protein structure are primary, secondary, tertiary, and quaternary. It is helpful to understand the nature and function of each level of protein structure in order to fully understand how a protein works. By Tracy Kovach. Created by Tracy Kim Kovach.

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Protein Structure

Everyone has heard of proteins. What are they on the molecular level? They're polymers of amino acids, of course. They make up most of your body, so we have to understand their structure very well! Check this out to learn the hierarchy of protein structure so that we can later learn all about what different types of proteins can do.

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Protein folding explained

Join DeepMind Science Engineer Kathryn Tunyasuvunakool to explore the hidden world of proteins.

These tiny molecular machines underpin every biological process in every living thing and each one has a unique 3D shape that determines how it works and what it does.

But figuring out the exact structure of a protein is an expensive and often time-consuming process, meaning we only know the exact 3D structure of a tiny fraction of the 200m proteins known to science.

Being able to accurately predict the shape of proteins could accelerate research in every field of biology. That could lead to important breakthroughs like finding new medicines or finding proteins and enzymes that break down industrial and plastic waste or efficiently capture carbon from the atmosphere.

Join Kathryn as she explains what protein folding is, why it's important and how our Artificial Intelligence system AlphaFold offers a solution to this grand scientific challenge.

Find out more:

deepmind.com/alphafold

Protein structure | Primary | Secondary | Tertiary | Quaternary

Primary structure is the linear sequence of amino acids written from the N termial of first to the C terminal of the last amino acid. The information of the primary structure is obtained by sequencing the gene or the protein. The primary structure further folds to form secondary structure. The most common secondary structure is the alpha helix and the beta sheet. secondary structure further forms tertiary structure. Interaction between tertiary structure forms quaternary structure.

Protein Folding

What are proteins made of and how do they get their shape? This animation is based on a great video made by DeLano Scientific LLC using PyMol. The original video lacked narration and was a bit quick for students to interpret. We have slowed it down and added a sound track and closed captioning. Our thanks to PyMOL for giving us permission to modify their video.

The French closed captions are courtesy of the Astound Group. Thanks for helping us!

Protein Folding Mechanism

Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil. Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by the ribosome, the linear chain begins to fold into its three dimensional structure. Folding begins to occur even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure (Anfinsen's dogma).[2] The energy landscape describes the folding pathways in which the unfolded protein is able to assume its native state. Experiments beginning in the 1980s indicate the codon for an amino acid can also influence protein structure.

The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded, so that protein dynamics is important. Failure to fold into native structure generally produces inactive proteins, but in some instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by incorrect folding of some proteins, because the immune system does not produce antibodies for certain protein structures.

Primary Structure :
The primary structure of a protein, its linear amino-acid sequence, determines its native conformation.[7] The specific amino acid residues and their position in the polypeptide chain are the determining factors for which portions of the protein fold closely together and form its three dimensional conformation. The amino acid composition is not as important as the sequence.[8] The essential fact of folding, however, remains that the amino acid sequence of each protein contains the information that specifies both the native structure and the pathway to attain that state. This is not to say that nearly identical amino acid sequences always fold similarly.[9] Conformations differ based on environmental factors as well; similar proteins fold differently based on where they are found.

Secondary Structure:
Formation of a secondary structure is the first step in the folding process that a protein takes to assume its native structure. Characteristic of secondary structure are the structures known as alpha helices and beta sheets that fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability. Alpha helices are formed by hydrogen bonding of the backbone to form a spiral shape (refer to figure on the right).The beta pleated sheet is a structure that forms with the backbone bending over itself to form the hydrogen bonds (as displayed in the figure to the left). The hydrogen bonds are between the amide hydrogen and carbonyl carbon of the peptide bonds.

Tertiary Structure

The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic portion and a hydrophobic portion. This property of secondary structures aids in the tertiary structure of a protein in which the folding occurs so that the hydrophilic sides are facing the aqueous environment surrounding the protein and the hydrophobic sides are facing the hydrophobic core of the protein.[11] Secondary structure hierarchically gives way to tertiary structure formation. Once the protein's tertiary structure is formed and stabilized by the hydrophobic interactions, there may also be covalent bonding in the form of disulfide bridges formed between two cysteine residues. Tertiary structure of a protein involves a single polypeptide chain; however, additional interactions of folded polypeptide chains give rise to quaternary structure formation.

Chaperone Concept : The Chaperones assist in the correct folding pattern of a protein.If Chaperone fails to do so then Protein ultimately becomes Prion protein which gives rise to several diseases lile Kuru , Scrapie disease and Alziemers.

Protein structure | primary secondary tertiary and quaternary structure of protein

Protein structure - This lecture explains about the protein structure hierarchy including primary, secondary, tertiary structures of protein. All the types of protein structures are explained in this video with example. So watch this video to understand alpha helix and beta sheet structure and the role of primary structure of the protein to make 3d protein which dictates the function of the protein.
So keep watching this video for knowing the following details
1. Primary structure of protein
2. Secondary structure of protein
3. Tertiary structure of the protein
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The protein folding problem: a major conundrum of science: Ken Dill at TEDxSBU

For 50 years, the protein folding problem has been a major mystery. How does a miniature string-like chemical -- the protein molecule - encode the functions of living organisms: how our muscles exert force, how our immune systems reject pathogens, how our eyes see our surroundings, how plants convert solar energy, and all the rest. Huge progress is being made. Moreover, these amazing nano-machines could play important roles in health and disease and commerce in the future.

In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group. These local, self-organized events are branded TEDx, where x = independently organized TED event. The TED Conference provides general guidance for the TEDx program, but individual TEDx events are self-organized.* (*Subject to certain rules and regulations)

Proteins

Paul Andersen explains the structure and importance of proteins. He describes how proteins are created from amino acids connected by dehydration synthesis. He shows the importance of chemical properties in the R-groups of individual amino acids in the polypeptide. He explains the four levels of protein folding and gives you an opportunity to fold proteins of your own using the game Foldit:

Download the video game foldit here:



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MBS 6250 Lehninger - Chapter 4 Proteins: Structure, Function, and Folding

Protein folding mechanism biochemistry

This lecture explains about the protein folding mechanism. The protein folding is most important to form an active site that is used for the enzyme catalysis. Proteins can never be functional without proper folding. In this video I explain how protein folding is done with the help of chaperone and protein folding assisting proteins and it also explains the puzzle behind the protein folding.
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Thank you for watching the video lecture on protein folding biochemistry.

What is a Protein? Learn about the 3D shape and function of macromolecules

A new version of this video is available at

Proteins play countless roles throughout the biological world, from catalyzing chemical reactions to building the structures of all living things.

Despite this wide range of functions all proteins are made out of the same twenty amino acids, but combined in different ways. The way these twenty amino acids are arranged dictates the folding of the protein into its unique final shape. Since protein function is based on the ability to recognize and bind to specific molecules, having the correct shape is critical for proteins to do their jobs correctly.

A PDF flyer accompanies this video at PDB-101 at

Animation by Maria Voigt, narration by Monica Sekharan
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Overview of protein structure | Macromolecules | Biology | Khan Academy

Primary, secondary, tertiary and quaternary protein structure. Thinking about how the different factors impacting a protein's structure. Beta pleated sheets. Alpha helices.

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AlphaFold: The making of a scientific breakthrough

The inside story of the DeepMind team of scientists and engineers who created AlphaFold, an AI system that is recognised as a solution to protein folding, a grand scientific challenge for more than 50 years.

Find out more:
deepmind.com/alphafold

Protein references:
TBP = To be published

1BYI: Sandalova, T., et al. (1999) Structure of dethiobiotin synthetase at 0.97 A resolution. Acta Crystallographica Section D 55: 610-624.
3NPD: Das, D. et al. (2014) Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family. Proteins 82: 1086-1092.
5AOZ: Bule, P., et al. Structural Characterization of the Third Cohesin from Ruminococcus Flavefaciens Scaffoldin Protein, Scab. (TBP)
5ERE: Joachimiak, A. A novel extracellular ligand receptor. (TBP)
5L8E: Dharadhar, S., et al. (2016) A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme. Journal of Structural Biology 196: 437-447.
5M20: Liauw, P., et al. Structure of Thermosynechococcus elongatus Psb32 fused to sfGFP. (TBP)
5W9F: Buchko, G.W., et al. (2018) Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides. Protein Science 27: 1611-1623.
6BTC: Mir-Sanchis, I., et al. (2018) Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements. Structure 26: 1144.
6CL6: Buth, S.A., et al. (2018) Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers. Viruses 10.
6CP9: Gucinski, G.C., et al. (2019) Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins. Structure 27: 1660.
6CVZ: Loppnau, P., et al. Crystal structure of the WD40-repeat of RFWD3. (TBP)
6D2V: Clinger, J.A., et al. Structure and Function of Terfestatin Biosynthesis Enzymes TerB and TerC. (TBP)
6E4B: Tan, K., et al. The crystal structure of a putative alpha-ribazole-5'-P phosphatase from Escherichia coli str. K-12 substr. MG1655 (CASP target). (TBP)
6EK4: Brauning, B., et al. (2018) Structure and mechanism of the two-component alpha-helical pore-forming toxin YaxAB. Nature Communications 9: 1806-1806.
6F45: Dunne, M., et al. (2018) Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition. Structure 26: 1573-1582.e4.
6M9T: Audet, M., et al. (2019) Crystal structure of misoprostol bound to the labor inducer prostaglandin E2receptor. Nature Chemical Biology 15: 11-17.
6MSP: Koepnick, B., et al. (2019) De novo protein design by citizen scientists. Nature 570: 390-394.
6N64: Birkinshaw, R.W., et al. Structure of SMCHD1 hinge domain. (TBP)
6N9Y: Kerviel, A., et al. (2019) Atomic structure of the translation regulatory protein NS1 of bluetongue virus. Nature Microbiology 4: 837-845.
6ORI: Spiegelman, L., et al. Enterococcal surface protein, partial N-terminal region (CASP target). (TBP)
6PX4: Krieger, I.V., et al. (2020) The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition. Journal of Molecular Biology 432: 4623-4636.
6QVM: Osipov, E.M., et al. Crystal structure of native O-glycosylated multiheme cytochrome cf with S-layer binding domain. (TBP)
6T1Z: Debruycker, V., et al. (2020) An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity. Nature Structural & Molecular Biology 27: 829-835.
6TRI: Rasmussen, K.K., et al. (2020) Revealing the mechanism of repressor inactivation during switching of a temperate bacteriophage. PNAS 117: 20576-20585.
6U7L: Minasov, G., et al. 2.75 Angstrom Crystal Structure of Galactarate Dehydratase from Escherichia coli. (TBP)
6UBL: Kosgei, A.J., et al. Structure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina. (TBP)
6UK5: Alvarado, S.K., et al. Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis. (TBP)
6VR4: Leiman, P.G., et al. Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2 (CASP target). (TBP)
6X6O: Shi, K., et al. (2020) Crystal structure of bacteriophage T4 Spackle as determined by native SAD phasing. Acta Crystallographica Section D 76: 899-904.
6XBD: Coudray, N., et al. Structure of MlaFEDB lipid transporter reveals an ABC exporter fold and two bound phospholipids. (TBP)
6YA2: Bahat, Y., et al. First structure of a glycoprotein from enveloped plant virus. (TBP)
6YFN: Rumnieks, J., et al. Expansion of the structural diversity of single-stranded RNA bacteriophages. (TBP)
6YJ1: Sobieraj, A., et al. (CASP target) Crystal structure of the M23 peptidase domain of Staphylococcal phage 2638A endolysin. (TBP)
7JTL: Flower, T.G., et al. (2020) Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion. Biorxiv.

Protein Structure Part 2: How and Why Do Proteins Fold?

This video explores how changes in amino acids determine protein structure, and how mutations can change protein organization and function. Students learn of the role of amino acid sequence in protein structure, how hydrogen bonding of the peptide backbone creates the secondary structure of proteins, and how intra- and intermolecular interactions define tertiary and quaternary structure respectively. Students also learn how keratins are assembled in hair.

This entire case study can be found on the National Center for Case Study Teaching in Science website at the following address:

Conformational stability: Protein folding and denaturation | MCAT | Khan Academy

Different bonds/interactions contribute to the stability of each level of protein structure. Let's explore some common ones such as peptide bonds, hydrogen bonds, and disulfide bonds. By Tracy Kovach. . Created by Tracy Kim Kovach.

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MCAT on Khan Academy: Go ahead and practice some passage-based questions!

About Khan Academy: Khan Academy offers practice exercises, instructional videos, and a personalized learning dashboard that empower learners to study at their own pace in and outside of the classroom. We tackle math, science, computer programming, history, art history, economics, and more. Our math missions guide learners from kindergarten to calculus using state-of-the-art, adaptive technology that identifies strengths and learning gaps. We've also partnered with institutions like NASA, The Museum of Modern Art, The California Academy of Sciences, and MIT to offer specialized content.

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Protein Structure/Folding AP Bio Topics 1.3, 1.4, 1.5

If you are interested in a notes/handout/worksheet I made to go with this video, check it out here:

Teaches the primary, secondary, tertiary, and quaternary structures of proteins while focusing on the bonds responsible. Also ends with a discussion of how mutations in the DNA can influence the overall shape and therefore function, of a protein.

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