Peptides. Structure and functions of proteins Department of General Chemistry Poznań University of Medical Sciences MD 2015/16

1.Peptides (glutathione, insulin) 2. Three dimensional structure of proteins: - primary, - secondary, - tertiary, - quaternary structure 3. Forces stabilizing the native conformation 4. Classification of proteins based on their composition

Glutathione – reduced GSH and oxidized GSSG (  -glutamylcysteinylglycine)

Structure of proteins - Primary – the linear sequence of amino acids linked together covalently. The primary structure is the one-dimensional first step in specyfying the three-dimensional structure of a protein. The strategy for determining the primary structure: - hydrolysis in HCl (concentrated HCl, 110 o C, 24 h), - Sanger reaction - Edman degradation - carboxypeptidases

Sanger’s reaction Sanger was the first to determine the sequence of a polypeptide. He reduced the disulfide bonds, separated the A and B chains, and cleaved each chain into smaller peptides using trypsin, chymotrypsin, and pepsin. Each peptide reacts with 1-fluoro-2,4-dinitrobenzene, which derivatizes the exposed  -amino group of amino terminal residues.

Structure of proteins - Secondary – refers to the arrangement in space of the atoms in the backbone of the polypeptide chain - Side chain groups are not included at the level of secondary structure - Forces stabilizing the secondary structure – hydrogen bonds of the peptide bond atoms

Hydrogen bonds in different helices

Hydrogen bonds formed between H and O atoms stabilize a polypeptide in an  -helical conformation

Amphipatic faces of a helice

Pleated  -sheets antiparallel

parallel Pleated  -sheets

A  -turn that links segments of antiparallel  sheet

Supersecondary structure of proteins   unit  unit  unit

Greek key  -meander

Collagen – connective tissue protein The repeating unit: (Gly-X-Pro) or (Gly-X-Hyp) Three individual helices are twisted around each other to form a stiff rod. Triple helical molecule ics called tropocollagen. The three strands are held together by hydrogen bonds.

Cross-link in collagen

Cross-link in elastin

Silk fibroin The regularly repeating sequence: (Ser-Gly-Ala-Gly) n Antiparallel pleated sheet

Structure of proteins Tertiary structure of proteins - includes the three-dimensional arrangement of all atoms in the protein, including the atoms in the side chains and any prosthetic groups (ones other than amino acids) - In very large proteins, the folding of parts of the chain can occur independently of the folding of other parts. Such independently folded portions of proteins are referred to as DOMAINS - Forces stabilizing – hydrogen bonds between side chains, electrostatic attractions (salt, ionic bonds), hydrophobic interactions,

Myoglobin One polypeptide chain,  -helix

Quaternary structure of proteins Proteins can consist of more than one polypeptide chain; they have more than one subunit. Quaternary structure – refers to the arrangement in space of subunits with respect to one another. Interaction between subunits is mediated by noncovalent forces, such as hydrogen bonds and hydrophobic interactions.

Hemoglobin: 4 polypeptide chains – 4 subunits (quaternary structure) Myoglobin: one polypeptide chain (tertiary structure)

Heme Hemoglobin

Forces involved in protein folding

CLASSIFICATION OF PROTEINS according to their shape Globular proteins – spherically shaped, compact, water soluble, most of globular proteins are soluble in the cytosol or in the lipid phase of biological membranes. Axial ratios (ratios of length to breadth) of less than 10 and generally not greater than 3-4. They are primary agents of biological actions: enzymes, transport molecules, hormones, membrane-bound receptors, immunoglobulins. Fibrous proteins – have relatively low water solubility, higher amount of the secondary structure, elongated „rodlike” shape, high tensile strength, unusual covalent cross-links. Fibrous proteins are generally insoluble in the cytosol. The axial ratios are greater than 10. They have mechanical and structural functions, provide mechanical support, a structural matrix, to individual cells and tissues of the mammalian organisms.

CLASSIFICATION OF PROTEINS ACCORDING TO THEIR COMPOSITION Simple proteins: contain only α-amino acids or their derivatives and occur as such in nature. Conjugated proteins: those which are united with some nonprotein substance (the prosthetic group)

SIMPLE PROTEINS: Albumins Globulins Histones Scleroproteins (albuminoids) Glutelins Prolamines Protamines

CONJUGATED PROTEINS: Nucleoproteins Glycoproteins and mucoproteins Phosphoproteins Chromoproteins Lipoproteins Metalloproteins

Denaturing agents: - form new hydrogen bonds stronger than native ones - reduce disulfide bonds Denaturation of proteins

Separation, isolation, purificaton of proteins

Electrophoresis of blood seum proteins Albumin  -  - and  - globulins

Electorophoretic separation of serum proteins