Levels Of Structure In Proteins

Viral Coat Proteins Of Spherical Viruses

The capsid proteins of a virus provide a protective shell around the enclosed RNA or DNA. These viral coats are made from an assembly of identical or nearly identical small protein subunits. The protein capsids of all known spherical viruses are built using icosahedral symmetry. In its simplest form, an icosahedron is a 20sided polygon with two, three, and fivefold symmetry, made from an arrangement of identical equilateral triangles .46A). Because constructing a protein subunit with equilateral threefold symmetry is difficult, the simplest known viruses contain three asymmetric subunits per triangle or 60 subunits per virus. Larger and more complex viral coats can be made by further subdividing these asymmetric units and using more protein subunits, all the while maintaining icosahedral symmetry. Viruses can be classified by their triangulation number which indicates the number of capsid subunits in multiples of 60. For example, a T = 1 virus has 60 subunits and a T = 3 virus has 3 × 60 = 180 subunits.

Viral capsid proteins. Illustration of an icosahedron showing two, three, and fivefold symmetry. Structure of the jellyroll sandwich fold of satellite tobacco necrosis viruscoat protein .

What Are Proteins Made Of

Proteins are polymers, meaning they are large molecules made up of many smaller molecules. The small molecules that make up proteins are called amino acids.

Each amino acid contains a carbon atom, an amino group, a carboxyl group, and a side chain .

The side chain is the only variable component of the amino acid. The type of side chain identifies the type of amino acid and also determines its characteristics . There are only about 20 different types of amino acid in the human body, but these can combine to make approximately 20,000 unique proteins.

Amino acids are joined together by peptide bonds, which form between the amino group of one molecule and the carboxyl group of another. Two amino acids joined together is called a dipeptide a chain made of multiple amino acids is known as a polypeptide.

Secondary Structure Of Protein

Secondary structure of protein refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone.

• The proteins do not exist in just simple chains of polypeptides.
• These polypeptide chains usually fold due to the interaction between the amine and carboxyl group of the peptide link.
• The structure refers to the shape in which a long polypeptide chain can exist.
• They are found to exist in two different types of structures helix and pleated sheet structures.
• This structure arises due to the regular folding of the backbone of the polypeptide chain due to hydrogen bonding between -CO group and -NH groups of the peptide bond.
• However, segments of the protein chain may acquire their own local fold, which is much simpler and usually takes the shape of a spiral an extended shape or a loop. These local folds are termed secondary elements and form the proteins secondary structure.

Secondary Structure of Protein

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Read A Brief Summary Of This Topic

protein, highly complex substance that is present in all living organisms. Proteins are of great nutritional value and are directly involved in the chemical processes essential for life. The importance of proteins was recognized by chemists in the early 19th century, including Swedish chemist Jöns Jacob Berzelius, who in 1838 coined the term protein, a word derived from the Greek prteios, meaning holding first place. Proteins are species-specific that is, the proteins of one species differ from those of another species. They are also organ-specific for instance, within a single organism, muscle proteins differ from those of the brain and liver.

Domains Motifs And Folds In Protein Structure

Proteins are frequently described as consisting of several structural units. These units include domains, motifs, and folds. Despite the fact that there are about 100,000 different proteins expressed in eukaryotic systems, there are many fewer different domains, structural motifs and folds.

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Introduction To Protein Structure

Proteins fold into stable threedimensional shapes, or conformations, that are determined by their amino acid sequence. The complete structure of a protein can be described at four different levels of complexity: primary, secondary, tertiary, and quaternary structure.

As a multitude of protein structures are rapidly being determined by Xray crystallography and by nuclear magnetic resonance , it is becoming clear that the number of unique folds is far less than the total number of protein structures. Not only do functionally related proteins generally have similar tertiary structures , but even proteins with very different functions are often found to share the same tertiary folds. As a consequence, structural conservation at the tertiary level is perhaps more profound than it is at the primary. The identification of the fold of a protein has therefore become an invaluable tool since it can potentially provide a direct extrapolation to function, and may allow one to map functionally important regions in the amino acid sequence.

What Are The 4 Levels Of Protein Structure

Posted June 22, 2020

The four levels of protein structure are primary, secondary, tertiary, and quaternary structure, which are distinguished from one another by the degree of complexity in the polypeptide chain.

• Primary structure: Primary structure describes the sequence of amino acids in the polypeptide chain, which is unique and specific to a particular protein.
• Secondary structure: Secondary structure refers to the highly regular local sub-structures derived from the coiling or folding of a polypeptide chain. There are two main types of secondary structures, the ?-helix and the ?-strand or ?-sheets, who are defined by pattern of hydrogen bonds between the main-chain peptide groups.
• Tertiary structure: Tertiary structure is the comprehensive three-dimensional structure of monomeric and multimeric protein molecules, where ?-helix and ?-sheets are further folded into a compact globular structure.
• Quaternary structure: Quaternary structure is the three-dimensional structure of a protein macromolecule formed by aggregation of two or more individual polypeptide chains. This protein macromolecule operates as a single functional unit, which is referred to as multimer, while each polypeptide chain is called a subunit.

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Primary Structure Of Proteins

Proteins are the most important and versatile class of macromolecules in the cell. The roles played by these molecules encompass anything from the transport of nutrients, catalyzing biochemical reactions to being structural components of cells or molecular motors. Proteins are linear polymers of amino acids connected by peptide bonds. They are synthesized from the template strand of DNA and contain unique and specific amino acid sequences in a linear form known as a primary structure.

Only twenty amino acids are necessary and sufficient for generating thousands of proteins in a cell. That does not mean there are only twenty amino acids. This is a common misconception. There are countless amino acids that exist in the world, but they are involved in other metabolic reactions but not protein synthesis. How individual protein gets its identity lies in the ordered combination of amino acids, which determines all its characteristics.

Tertiary Structure Of Protein

• This structure arises from further folding of the secondary structure of the protein.
• H-bonds, electrostatic forces, disulphide linkages, and Vander Waals forces stabilize this structure.
• The tertiary structure of proteins represents overall folding of the polypeptide chains, further folding of the secondary structure.
• It gives rise to two major molecular shapes called fibrous and globular.
• The main forces which stabilize the secondary and tertiary structures of proteins are hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces of attraction.

Tertiary Structure of Protein

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The Iglike Family Of Transcription Factors

The structures of several families of Iglike transcription factors have been elucidated .6). Each of them uses an Iglike fold with C2type topology to bind DNA through loop regions at one end of the sandwich . The SCOP database classifies these proteins as the superfamily of p53like transcription factors . Although the individual structures and binding modes vary somewhat among these families, three common loops are used by all six families to contact DNA . The loop between strands A and B interacts with the major groove, making sequencespecific contacts. The loop between strands E and F contacts the DNA backbone, in some cases making basespecific contacts in the minor groove, and the Cterminal tail emanating from strand G sits in the major groove, making basespecific contacts. The structural details of these families are described below.

p53 Tumor Suppressors

The first of these families to be examined structurally, p53 tumor supressors ,6), can bind DNA as a monomer . p53 tumor suppressors are key proteins facilitating protection against many types of cancer in animals. It is estimated that up to onehalf of all cancers involve genetic inactivation of p53 . In this structure, the major groovebinding Cterminal tail is an helix and the EF loop is stabilized by a zinc atom .

NFB

NFAT

CBF

TDomain

STAT Proteins

What Is The Tertiary Structure Of A Protein

The tertiary structure of a protein refers to the overall three-dimensional arrangement of its polypeptide chain in space. It is generally stabilized by outside polar hydrophilic hydrogen and ionic bond interactions, and internal hydrophobic interactions between nonpolar amino acid side chains (Fig.

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Structural Classifications Of Proteins

Protein structures can be grouped based on their structural similarity, topological class or a common evolutionary origin. The Structural Classification of Proteins database and CATH database provide two different structural classifications of proteins. When the structural similarity is large the two proteins have possibly diverged from a common ancestor, and shared structure between proteins is considered evidence of homology. Structure similarity can then be used to group proteins together into protein superfamilies. If shared structure is significant but the fraction shared is small, the fragment shared may be the consequence of a more dramatic evolutionary event such as horizontal gene transfer, and joining proteins sharing these fragments into protein superfamilies is no longer justified. Topology of a protein can be used to classify proteins as well. Knot theory and circuit topology are two topology frameworks developed for classification of protein folds based on chain crossing and intrachain contacts respectively.

Immunoglobulins And Immunoglobulinlike Superfamilies

Traditionally, the term immunoglobulin fold refers to the homologous domain structures present in the variable and constant regions of all immunoglobulins. In recent years, however, with the rapid growth of sequence and structure knowledge, many other proteins whose functions are not related to immunoglobulins have nonetheless been found to contain one or more Iglike domains in their tertiary structures. Examples of such proteins include the cell surface glycoprotein receptors such as growth hormone receptor, CD4 and CD8, adhesion molecules such as cadherins and type III fibronectins, class I and class II major histocompatibility proteins, chaperone protein PapD, the transcriptional factor NFB, and even some enzymes such as Cu and Zn superoxide dismutase and galactosidase. The discovery of the Iglike domains in many proteins not only broadens the definition of superfamily, but more importantly, demonstrates the versatility of the fold and the ability of these domains to function as modular units in many diverse systems.

Tertiary and secondary structures of immunoglobulin fold. The coordinates used for the ribbon diagrams are taken from the PDB entries 3hfl , 1hnf , 1fna , 1 + tlk , and 1gof .

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Frequently Observed Secondary Structure Assemblies Or Structural Motifs

This section describes some structural motifs commonly observed in a wide variety of proteins. Other structural motifs of particular functional significance, such as DNA and RNAbinding motifs, are described in later sections of this unit.

Helix Bundles

CoiledCoil

As a special case of helix bundles, coiledcoil refers to two or more helices intertwined with each other to form a supercoiled helical structure. The helices involved in a coiledcoil configuration are normally long, with certain characteristic repeats in their amino acid sequences, and are usually parallel rather than antiparallel to each other. In most cases, the participating helices of a coiledcoil are from separate subunits but reside in a topologically equivalent part of a protein.

Hairpin

When an antiparallel sheet contains only two strands connected by a single tight turn, it is termed a hairpin .1G). A hairpin is usually highly twisted and less regular compared to a more extended sheet.

Greek Key and JellyRoll Motifs

Sandwich

Mixed / Sandwich

Aside from the sandwich, other layered secondary structure assemblies include /, //, and // sandwiches. For example, an //sandwich is defined as structures with one layer of sheet sandwiched in between two layers of helix. Both layers of helix pack closely against the middle sheet layer. The /// sandwich is commonly observed in nucleotidebinding proteins .

Barrel

/Barrel

Propeller

Structure Of Immunoreceptorligand Complexes

The goal of structural immunology in recent years has been to define molecular structures of immunoreceptorligand complexes rather than revealing new protein folds. The notable milestones include the publications of several T cell receptors and their cognate MHCpeptide complexes i.e., T cell coreceptor CD8 or CD4 and their class I or II MHC complexes , T cell coreceptor CTLA4 and ligand B7 complex , NK cell killer immunoglobulinlike receptor and its MHC ligand complexes , NK cell activating receptor NKG2D and its ligand complexes , and Fc receptors in complex with their Fc ligands .

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Quaternary Structure Of Protein:

• Some proteins are composed of more than one polypeptide chain. Each polypeptide chain in such protein are called sub-units.
• The quaternary structure refers to interaction between these sub-units to form large final 3D structure. Therefore, quaternary structure is interaction between different polypeptide chains of multi chain protein.
• Quatarnary structure is found only in protein which are composed of more than one polypeptide chains such as hemoglobin
• Bonds like H-bond, ionic bond, hydrophobic interaction helps to from quaternary structure.

Problem : Tertiary Structure Of A Protein

Tutorial to help answer the question

The tertiary structure of a protein refers to the:

A. Sequence of amino acids

B. Presence of alpha-helices or beta-sheets

C. Unique three dimensional folding of the molecule

D. Interactions of a protein with other subunits of enzymes

E. Interaction of a protein with a nucleic acid

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Levels Of Protein Organization

A protein’s primary structure is defined as the amino acid sequence of its polypeptide chain secondary structure is the local spatial arrangement of a polypeptide’s backbone atoms tertiary structure refers to the three-dimensional structure of an entire polypeptide chain and quaternary structure is the three-dimensional arrangement of the subunits in a multisubunit protein. In this series of pages we examine the different levels of protein organization. We also view structures in lots of ways — C backbone, ball-and-stick, CPK, ribbon, spacefilling — as well color is used to highlight different aspects of the amino acids, structure, etc. As you traverse though this module please note these aspects.

This module includes links to KiNG , which displays three-dimensional structures in an animated, interactive format. These “kinemages” can be rotated, moved, and zoomed, and parts can be hidden or shown. Kinemages were originally implemented under the auspices of the Innovative Technology Fund and the Protein Society, and the programming and maintenance are done by David C. Richardson and Jane S. Richardson.

Reference: “THE KINEMAGE: A TOOL FOR SCIENTIFIC COMMUNICATION” D.C. Richardson and J.S. Richardson Protein Science 1: 3-9. Also Trends in Biochem. Sci. 19: 135-8.

Text adapted from: Demo5_4a.kin

Classes Of Protein Structure

The function of a protein depends heavily on its final structure. Tertiary and quaternary proteins are both functional proteins with a 3D structure. However, the type of structure can vary significantly between different proteins.

There are two main classes of 3D protein structure: globular proteins and fibrous proteins.

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Analysis Of Protein Structure

The complexities of a protein structure do make the elucidation process of a complete protein structure extremely difficult, even with the most advanced analytical equipment. An amino acid analyzer can be used to determine which amino acids are present and their molar ratios. The sequence of the protein can then be analyzed by means of peptide mapping, and the use of Edman degradation. This process is routine for peptides and small proteins but more complex for large multimeric proteins.

One method which is used to characterize the secondary structure of a protein is called circular dichroism spectroscopy. The different types of secondary structure, -helix, ß-sheet, and random coil, all have characteristic circular dichroism spectra in the far-UV region of the spectrum. To determine the three-dimensional structure of a protein by X-ray diffraction, a large and well-ordered single crystal is required. X-ray diffraction allows the measurement of the short distance between atoms and it yields a three-dimensional electron density map, which can be used to build a model of the protein structure.

Types Of Beta Sheets Observed In Proteins

1) Parallel beta sheet – All bonded strands have the same N to C direction. As a result they have to be separated by long sequence stretches. The hydrogen bonds are equally distanced.

The figure to the left shows a three-stranded parallel beta sheet from the protein thioredoxin. The three parallel strands are shown in both cartoon format and in stick form containing backbone atoms N, CA, C, and O’ . Hydrogen bonds are identified by arrows connecting the donor nitrogen and acceptor oxygens. Strands are numbered according to their relative position in the polypeptide sequence.

2) Antiparallel beta sheet – The beta strands run in alternating directions and therefore can be quite close on the primary sequence. The distance between successive hydrogen bonds alternates between shorter and longer.

The figure to the right shows a three-stranded antiparallel beta sheet from thioredoxin. The three antiparallel strands are shown in both cartoon format and in stick form containing backbone atoms N, CA, C, and O’ . Hydrogen bonds are identified by arrows connecting the donor nitrogen and acceptor oxygens. Strands are numbered according to their relative position in the polypeptide sequence.

3) Mixed beta sheet – a mixture of parallel and antiparallel hydrogen bonding. About 20% of all beta sheets are mixed.

Some of the main features of beta sheets include:

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