1. Proteins By Dr. Gobinath Pandian

2. Proteins are the machines that drive cells and, ultimately, organisms. Proteins are composed of individual units called amino acids. Amino acids all share a similar structure. The difference between them is the so-called "R" group. The "R" group is the cluster of atoms that give an amino acid its particular characteristics. Introduction

3. Proteins are not linear molecules as suggested when we write out a "string" of amino acid sequence, -Lys-Ala-Pro-Met-Gly- etc., for example. Rather, this "string" folds into an intricate three- dimensional structure that is unique to each protein. It is this three-dimensional structure that allows proteins to function. Thus in order to understand the details of protein function, one must understand protein structure.

4. Formation of Peptide Bond in AA ↓ ↓ → H 2 O Peptide Bond

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6. Amino Acids The amino acid residues of proteins are defined by an amino group and a carboxyl group connected to an alpha carbon to which is attached a hydrogen and a side chain group R. The smallest amino acid, glycine, has a hydrogen atom in place of a side chain. All other amino acids have distinctive R groups. Because the alpha carbon of the other amino acids have four different constituents, the alpha carbon atom is an asymmetric center and most naturally occurring amino acids are in the L form. (S)- Alanine (left) (S)-Alanine (left) and (R)-alanine (right) in zwitterionic form at neutral pH (R)-alanine (Right)

7. Any number of amino acids can be joined together to form peptides of any length. Small peptides (containing less than a couple of dozen amino acids) are sometimes called oligopeptides. Longer peptides are many times called polypeptides. Notice that peptides have a "polarity"; each peptide has only one free a-amino group (on the amino-terminal residue) and one free (non- sidechain) carboxyl group (on the carboxy- terminal residue)

8. Amino acids fall into several naturally occurring groups including hydrophobic, hydrophilic, charged, basic, acidic, polar but uncharged, small polar, small hydrophobic, large hydrophobic, aromatic, beta-branched, sulfur containing etc. Hydrophobic amino acids, sometimes called non-polar amino acids, reside primarily on the interior of the protein. Hydrophilic amino acids, sometimes called polar amino acids, reside primarily on the exterior of the protein. Many amino acids will fall into more than one group since each amino acid side chain has several properties.

9. Forces determining protein structure Several covalent and non-covalent forces determine protein structure. 1)van der Waals interactions 2) Hydrophobic force 3)Electrostatic forces 4)Dipole moments 5)Hydrogen bonds 6)Covalent bond

10. 1. Van der Waals interactions interactions between immediately adjacent atoms: These non-covalent forces result from the attraction of one atoms nucleus for the electrons of another atom in a non-covalent form (no sharing of orbitals). These forces are much weaker than covalent interactions and the interaction distances are much longer than covalent bonds and much shorter than the other non- covalent interactions. Van der Waals interactions are non-directional and very weak. However, significant energy of stabilization can be obtained in the central hydrophobic core of proteins by the additive effect of many such interactions.

11. 2.Hydrophobic force The hydrophobic force is really a negative non-covalent force. The presence of hydrophobic side chains in aqueous solution induces the formation of structured water (clathrate cages of water molecule form, like miniature ice crystals about the hydrophobic side chains). The hydrophobic force is one of the largest determinants of protein structure. Most secondary structural elements we will discuss have an amphipathic nature, one hydrophobic side and one hydrophilic surface of the protein.

12. 3.Electrostatic forces The attraction of oppositely charged side chains can form salt- bridges that stabilize secondary and tertiary structures. The electrostatic force is quite strong, falling off as the square of the distance between the charged atoms. It also depends heavily on the dielectric constant of the medium in which the protein is dissolved. It is strongest in a vacuum and 80 fold weaker in water and weaker still at elevated salt solutions. Water and ions can shield electrostatic interactions reducing both their strength and distance over which they operate.

13. 4.Dipole moments Dipole moments are caused by pairs of charges separated by a larger distance than permitting a salt- or ion bridge. The dipole moment gives rise to an electric field along the entire length of a structural element. Dipole moments are often used by proteins to attract and position charged substrates and products. The peptide chain naturally has a dipole moment because the N- terminus carries about 1/2 a positive charge and the C-terminus carries about 1/2 unit of negative charge. The alpha helix is known to carry a partial negative charge at its C- terminus and a positive charge at its N-terminus. In order to help neutralize this charge distribution, alpha helices often have acidic residues near their N-terminus and a basic residue near their C-terminus.

14. 5. Hydrogen bonds Hydrogen bonds occur when a pair of nucleophilic atoms such as oxygen and nitrogen share a hydrogen between them. The hydrogen may be covalently attached to either nucleophilic atom (the H-bond donor) and shared with the other atom (the H-bond receptor). H-bonds are directional and their strength deteriorates dramatically as the angle changes. Hydrogen bonds do not, in general, contribute to the net stabilization energy of proteins because the same groups that hydrogen bond to each other in a native protein structure, can hydrogen bond to water in the denatured state. However, hydrogen bonds are extremely important because of their directionality, they can control and limit the geometry of the interactions between side-chains. This is shown most dramatically in patterns of hydrogen bonding between the carboxyl groups and the amino groups in the peptide backbone that give rise to alpha helix and beta strand conformations.

15. 6. Covalent bond The major properties of the covalent bonds hold proteins together are their bond distances and bond angles. In particular, the bond angles between two adjacent bonds on either side of a single atom, or the dihedral angles between three contiguous bonds and two atoms control the geometry of the protein folding.

16. Primary structure refers to the "linear" sequence of amino acids. Primary structure is sometimes called the "covalent structure" of proteins because, with the exception of disulfide bonds, all of the covalent bonding within proteins defines the primary structure. Generally, peptides are small 10 or 20 residues; polypeptides might range up to 50 or 60 residues, Primary Structures- Protein

17. Small peptides (containing less than a couple of dozen amino acids) are sometimes called oligopeptides. Longer peptides are many times called polypeptides. each peptide has only one free a-amino group (on the amino- terminal residue) and one free (non-sidechain) carboxyl group (on the carboxy-terminal residue):

18. Primary Structure of Protein

20. Secondary Structures (SS) Secondary structure is the initial folding pattern (periodic repeats) of the linear polypeptide. There are 2 main types of secondary structure: α- helix and β-sheet Secondary structures are stabilized by hydrogen bonds.

21. The α-helix The α-helix is right-handed or clock-wise (for L isoforms left-handed helix is not viable due to steric hindrance) Each turn has 3.6 aa residues and is 5.4 Ao high. The helix is stabilized by H-bonds between –N-H and –C=O groups of every 4th amino acid. α-helices can wind around each other to form ‘coiled coils’ that are extremely stable and found in fibrous structural proteins such as keratin, myosin (muscle fibers) etc

22. The α-helix Structure

23. Five different kinds of constraints affect the stability of an a helix: The electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups. The bulkiness of adjacent R groups. The interactions between amino acid side chains spaced three (or four) residues apart. The occurrence of Pro and Gly residues. The interaction between amino acid residues at the ends of the helical segment and the electric dipole inherent to the a helix.

24. β-Pleated Sheet Extended stretches of 5 or more aa are called β- strands. β-strands organized next to each other make β-sheets. If adjacent strands are oriented in the same direction (N- end to C-end), it is a parallel β-sheet, if adjacent strands run opposite to each other, it is an antiparallel β-sheet. There can also be mixed β-sheets. The H-bonding pattern varies depending on type of sheet. β-sheets are usually twisted rather than flat. Fatty acid binding proteins are made almost entirely of β-sheets

25. β-Pleated Sheet

26. Tertiary Structure 3D folding or ‘bundling up’ of the protein is the tertiary structure of the proteins. Non-polar residues are buried inside, polar residues are exposed outwards to aqueous environment. Many proteins are organized into multiple ‘domains’ which are compact globular units that are connected by a flexible segment of the polypeptide. Each domain contributes a specific function to the protein. Different proteins may share similar domain structures, eg: kinase-, cysteine-rich-, globin-domains.

27. Tertiary Structures The protein then can compact and twist on itself to form a mass called it’s Tertiary Structure

28. 5 kinds of bonds stabilize tertiary structure H-bonds, van der waals interactions, hydrophobic interactions, ionic interactions and disulphide linkages In disulphide linkages, the SH groups of two neighboring cysteines form a –S-S- bond called as a disulphide linkage. It is a covalent bond, but readily cleaved by reducing agents that supply the protons to form the SH groups again.

29. Quaternary Structure. Quaternary structure is a larger assembly of several protein molecules or polypeptide chains, usually called subunits in this context. The quaternary structure is stabilized by the same non-covalent interactions and disulfide bonds as the tertiary structure. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers.

30. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, and a tetramer if it contains four subunits. The subunits are frequently related to one another by symmetry operations, such as a 2-fold axis in a dimer. Multimers made up of identical subunits are referred to with a prefix of different subunits are referred to "hetero-" (e.g. a heterotetramer, such as the two alpha and two beta chains of hemoglobin). Many proteins do not have the quaternary structure and function as monomers.

31. Protein Structures Overview

32. Several Proteins then can combine and form a protein’s Quaternary Structure

33. Functions of Protein What does Protein Do? Protein has a large number of important functions in the human body—and in fact, the human body is about 45% protein. It’s an essential macromolecule without which our bodies would be unable to repair, regulate, or protect themselves. Proteins are, in effect, the main actioners in cells and in an entire organism. Without proteins the most basic functions of life could not be carried out. Respiration, for example, requires muscle contractions, and muscle contractions require proteins.

34. Protein has a range of essential functions in the body, including the following: Required for building and repair of body tissues (including muscle) Enzymes, hormones, and many immune molecules are proteins Essential body processes such as water balancing, nutrient transport, and muscle contractions require protein to function. Protein is a source of energy. Protein helps keep skin, hair, and nails healthy. Protein, like most other essential nutrients, is absolutely crucial for overall good health.

35. Proteins as Enzymes The function of proteins as enzymes is perhaps their best- known function. Enzymes are catalysts—they initiate a reaction between themselves and another protein, working on the molecule to change it in some way. The enzyme, however, is itself unchanged at the end of the reaction. Enzymes are responsible for catalyzing reactions in processes such as metabolism, DNA replication, and digestion. In fact, enzymes are known to be involved in some 4,000 bodily reactions.

36. Proteins in Cellular Signaling and Molecular Transport Cells signal one another for an enormous variety of reasons, the most basic of which is simply to coordinate cellular activities. Signaling is how cells communicate with one another, allowing such essential processes as the contraction of the heart muscle to take place. Proteins are important in these processes due to their ability to bind other molecules—a protein produced by one cell may bind to a molecule produced by another, thus providing a chemical signal which allows the cells to provide information about their state. Proteins are also involved in molecular transport. A prime example of this is the protein called hemoglobin, which binds iron molecules and transports them in the blood from the lungs to organs and tissues throughout the body.

37. Structural proteins are those which confer strength and rigidity to biological components which would otherwise be unable to support themselves. Structural proteins tend to have very specific shapes— long, thin fibers or other shapes which, when allowed to form polymers, provide strength and support. Structural proteins are essential components of collagen, cartilage, nails and hair, feathers, hooves, and other such components. Structural proteins are also essential components of muscles, and are necessary to generate the force which allows muscles to contract and move.

38. http://www.youtube.com/watch?v=lY0A6cq2ug A&feature=related