Proteins Levels of structural organization Structural diversity Professor E.V. Lukasheva Russian Peoples’ Friendship University Medical Faculty Department of Biochemistry Biochemistry

Proteolytic enzymes (proteases) catalyze the destruction of proteins and peptides (hydrolysis of peptide bonds) Uncommon bonds: glutathione Unusual Amino Acids: carnosine, anserine (beta-alanyl-histidine), thyroliberin (pyro-Glu- Pro-His) Cyclization: cyclosporin somatostatin, endorphins, enkephalins The ways to protect peptides against proteolysis - the inclusion in their molecule

Resistance to proteolysis is increased by incorporating into the molecule abnormal bonds or abnormal amino acids In glutathione the bond between glutamate and cysteine is formed not by alpha, but by gamma-carboxyl group

Thyrotropin (pyro-Glu-gis-pro) - contains cyclized glutamic acid

Cyclosporine – cyclization of polypeptide chain

Somatostatin contains a cyclic structure, formed by a disulfide bond between amino acid residues of cysteine. ​ ​

Levels of Protein Structure I. Primary structure of proteins - a sequence of amino acids in the polypeptide chain, which is determined by the genetic code. ~ 5000 AA - the longest chain ~ 2000 AA - common proteins ~ 50 AA - small proteins (MW ~ 6000 Da) Example - Insulin 51 AA (M.M.5733 Da) Amusing feature of the collagen primary structure - each third amino acid is glycine.

II. The secondary protein structure is created by the hydrogen bonds between the polypeptide chains Energy of covalent bonds > 400 kJ / mol Hydrogen bond energy kJ / mol In protein molecule there are many hydrogen bonds, so they form stable structures. The main types of secondary structure are 1) alpha helices 2) beta-sheets

α-Helix is twisted right. = C = O group of one AA forms hydrogen bond with the – NH 2 - group of the fourth amino acid following in polypeptide chain (1 turn of the helix includes 3.6 amino acid residues) Inside the spiral there is no empty space. Hdrogen bonds are parallel to the axis of the helix.

 - folded layers

III. Tertiary structure describes the packing of alpha-helices, beta- sheets and random coils with respect to each other on the level of one whole polypeptide chain (packing of the whole polypeptide chain in the space). is formed with the participation of different types of links:

1) ion (electrostatic interaction) 2) hydrogen 3) interaction of the hydrophobic side chains of amino acids to each other. covalent 4) (S-S) disulfide

Tertiary structure of insulin molecule

Cytochrome C

Transmembrane protein

Collagen : three left-handed helices form triple helix twisted right

IV. Quaternary structure - a method of several polypeptide chains packing in space. Quaternary structure only exists, if more than one polypeptide chain is present in a protein and is formed using the same types of bonds as the tertiary structure.

Hemoglobin: four polypeptide chains (protomers) form a whole oligomeric molecule

Cytochrome b6f

Domein - is usually defined as a modular functional unit folding independently, structurally separate part of the polypeptide chain that performs a specific function. In proteins of different organisms that perform similar functions there are common "standard" domains. For example, the dehydrogenases (~ 200 are known presently) have a binding domain for coenzyme NAD+. Motifs and domains are combinations of secondary structures. Motifs only consist out of few secondary structures and may but need not have a function. A domain is more complex. It is usually defined as a modular functional unit folding independently.

Transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA.DNAproteinDNA sequencestranscriptionmessenger RNA

Protein folding – the adoption of the native conformation of protein (the polypeptide chain is packed into three- dimentional structure and the protein becomes functionally active) Protein denaturation - the loss of their three dimensional structure and thus their function. Proteins can be denatured through exposure to heat or chemicals.

Chaperones are proteins which provide folding of the newly synthesized polypeptide chains or partially denatured protein Prevent protein denaturation Facilitate the adoption of their native conformation are linked to the protein until it is delivered to the place of manifestation of its activity in a cell Chaperones were discovered as heat shock proteins and often are named hsp.

Chaperones

Bacterial chaperones GroES and GroEL (top view). The new-synthesized protein enters the central cavity, where it takes its native structure.

Protein Misfolding and Degenerative Diseases Diseases associated with the "wrong" folding of proteins lead to the deposition of nproteins in tissues in the form of huge conjugates. Alzheimer's Disease Prion diseases

The word prion, coined in 1982 by Stanley B. Prusiner, is derived from the words protein and infection. proteinaceous –infective –on – particle.Stanley B. Prusiner Normal folding (а) Alpha-helices 35 kDa Prion folding (б) “pathologic conformation”: beta-sheets +

Prion diseases

A prion is an infectious agent composed of protein in a misfolded forminfectious agentproteinmisfolded This would be in contrast to all other known infectious agents, like viruses, bacteria, fungi or parasites—which must contain nucleic acids (either DNA, RNA, or both).virusesbacteriafungiparasitesnucleic acidsDNARNA Prions are responsible for the transmissible spongiform encephalopathies in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle. In humans, prions cause Creutzfeldt- Jakob Disease (CJD), variant Creutzfeldt-Jakob Disease (vCJD), Gerstmann– Sträussler–Scheinker syndrome, Fatal Familial Insomnia and kuru. All known prion diseases in mammals affect the structure of the brain or other neural tissue and all are currently untreatable and universally fatal. In 2013, a study revealed that 1 in 2,000 people in the United Kingdom might harbour the infectious prion protein that causes vCJD.transmissible spongiform encephalopathiesmammalsbovine spongiform encephalopathycattleCreutzfeldt- Jakob DiseaseGerstmann– Sträussler–Scheinker syndromeFatal Familial Insomniakurumammalsbrainneural Kuru is an incurable degenerative neurological disorder endemic to tribal regions of Papua New Guinea. It is a type of transmissible spongiform encephalopathy Prion diseases could play the role of intraspecific protection factor from the spread of cannibalism.

The function of proteins in the body 1.Nutritious. casein milk g protein/day - this is normal for an adult 2. Catalytic. Enzymes - biological catalysts of protein nature. 3.Protective function. The immune system – antibodies 4.Coagulation and anticoagulation system in blood. 5.Transport. (Hemoglobin - O 2, lipoproteins - carry fat- soluble vitamins, lipids, steroid hormones)

6. Contractility. Muscle proteins actin, myosin Construction. Proteins are components of cellular membranes - cytoskeleton. Proteins are the the basis of bone (skeleton). 8. Hormonal function. Hormones: the protein (insulin, glucagon,...), peptide (oxytocin, vasopressin,...), amino acid derivatives (epinephrine, thyroxine,...). 9. Receptors. Proteins are endowed with the capacity for recognition and binding: antibody-antigene, hormone - receptor...)