Protein_structure_M2P_202425.pptx

PROTEIN STRUCTURE AND FUNCTION M2P Fall 2024 Wendy S. Innis, Ph.D. [email protected] Session Objectives Describethe bonds and forces that facilitate formation of different protein structures and interactions with other biomolecules Differentia...

PROTEIN STRUCTURE AND FUNCTION M2P Fall 2024 Wendy S. Innis, Ph.D. [email protected] Session Objectives Describethe bonds and forces that facilitate formation of different protein structures and interactions with other biomolecules Differentiate between primary, secondary, tertiary, and quaternary protein structures Outline the molecular machinery required for protein folding and denaturation Compare and contrast the structural and functional features of fibrous proteins Explain how abnormal protein structure affects function and can cause disease Describe the technologies and methods used to evaluate proteins and their importance in medicine Levels of protein structure At each level there are forces that stabilize and facilitate structure Increasing structure complexity  Globular Fibrous Hemoglobin Collagen Linear with repeating unit MAJOR structure PROTEIN β-adrenergic receptor STRUCTURAL Water soluble CLASSIFICATIO NS Zinc finger transcription factor Distinct domain that binds to the One or more regions aligned to major or minor groove in DNA cross the lipid membrane DNA binding Transmembrane Primary protein structure The primary structure is the linear sequence of amino acid residues joined through peptide bonds 3-D structure of a polypeptide is determined by its primary structure Peptide bonds Condensation rxn (dehydration) between α- carboxylate group on one amino acid and α-amino group of another amino acid Peptide bond characteristics affect protein structure Peptide bond rotation is restricted; resonance Carbonyl & amide of peptide bond exhibit strong electronegativity Rigid and planar with little bond rotation Side chains exist in trans configuration to prevent steric hindrance Limits secondary and tertiary resonance due to structures that can be formed from the electron polypeptide chain delocalization Chemical nature of the amino acids Aliphatic (nonpolar) R-groups Non-aromatic with hydroxyl R-groups Sulfur-containing R-groups Acidic amino acids and their amides Basic amino acids Aromatic rings Imino acids Nonpolar (aliphatic) side groups: gly (-H) ala, ile, leu, val (hydrocarbon side chains) phe, trp (aromatic side chains) met (thioether group) pro (5-member ring including a-amino group— secondary, not primary, amino acid; IMINO acid) Side chains with basic groups (proton acceptors): arg, lys, his Side chains with acidic groups (proton donors): asp, glu Polar but uncharged groups: amide derivatives of asp and glu: asn, gln Polar but uncharged groups: hydroxyl groups: ser, thr, tyr (also aromatic); cys has sulfhydryl instead of hydroxyl Polar but uncharged groups: cys has sulfhydryl instead of hydroxyl in ser, and oxidizes to cystine Other classifications: Hydrophilic vs hydrophobic OPTICAL properties—dextrorotatory, levorotatory; L-amino acids, not D-; UV absorbance of aromatic amino acids Essential vs non-essential (conditionally non-essential) Glucogenic vs ketogenic, or ketogenic/glucogenic (catabolic classification) Proteogenic non-standard amino acids: selenocysteine, pyrrolysine No dedicated codon, by added in place of a stop codon when additional specific sequence is present (SECIS element = selenocysteine) Non-proteinogenic amino acids: non-coded, but occur naturally in proteins (or elsewhere in nature); ornithine, D-amino acids, etc. Post-translationally modified Secondary structure H-bonding of peptide backbone causes the amino acids to fold into a repeating pattern Common (regular) structures are α-helix and β-sheet “Random coil” – undefined irregular secondary structure; no inherent 3D structure Secondary structures:  Secondary structures: Beta (β-)sheet stabilized by hydrogen bonds co-planar with β-pleat hydrogen bonds in different regions of the polypeptide R groups alternately project above & below plane of the sheet Super secondary structures (motifs) Globular proteins are constructed by combining secondary structural elements Pattern of secondary structure elements recognized in multiple proteins= motif  motif most common super-secondary structure nonrepetitive structures (turns, coils, and loops) Tertiary structure Final folded state of a complete polypeptide in 3-D conformation Stabilized by Hydrophobic interactions: attraction between closely packed hydrophobic/nonpolar groups Binding Hydrogen bonding: interaction between proton donors site for and acceptors (aqueous environment) oxygen Ionic interactions: charge-charge, salt-bridges Disulfide bond formation: oxidation of nearby sulfhydryl groups Creates specific and flexible binding sites for ligands Maintains appropriate surface for the protein’s cellular location Overall shapes in general: fibrous or globular Folding can be affected by post-translational Polar amino acids on the modifications of amino acids: phosphorylation, periphery glycosylation, acetylation, more Protein Domains Fundamental functional and three- dimensional structural unit(s) of a polypeptide Typically comprised of one or more super-secondary structure Folding of a domain usually occurs independently of folding in other domains A) Secondary structure often packs into motifs—stable easily-folded arrangements, cannot exist independently B) Domain is a conserved part of a given full-length protein sequence, with defined tertiary structure that can evolve, function and exist independently of the rest of the protein chain; each domain forms a compact 3D structure and can often be independently stable and folded usually within a distinct function C) Large proteins usually made up of several independently folded domains Protein folding requires energy Chaperone proteins protect and assist in proper folding of nascent polypeptide chains, during or after synthesis Also assist in refolding after partial denaturation Participate in translocation to appropriate cellular locales Facilitating the proper interactions for folding requires ATP Primary structure determines folding (3D conformation) Quaternary structure Multiple polypeptide chains (or subunits) assembled into a supra- molecular complex Number of subunits designated by prefix, i.e., dimeric (2), trimeric (3), etc. May consist of identical (homopolymeric) or different (heteropolymeric) subunits Hemoglob in Protein misfolding and function Protein misfolding alters normal function and interactions of proteins Hemoglobin – quaternary structure, tetramer with 2 α and 2 β subunits In sickle cell anemia, a mutation at position 6 in the primary structure of the β chain has Val substituted for Glu Val-6 binds to different hydrophobic area, changing tertiary structure of the β subunit, and modifies overall quaternary structure  Generally insoluble in water Elongated, rigid proteins enriched in specific amino acids and unique secondary structures Fibrous Proteins Exhibit unique mechanical properties and serve structural functions in the body Most structural proteins are fibrous Collagen Polymerization of collagen molecules forms collagen fibrils Superfamily of extracellular matrix proteins that provide tensile strength Most abundant protein in the body Triple helix of three α- polypeptides wound around each other Collagen synthesis Collagen primary structure Polymer of (Gly-X-Y) repeats, where X is frequently proline and Y is often hydroxyproline (or hydroxylysine) Pro and Lys are important for collagen function α chains are held together by interchain Vitamin C required cofactor for the hydroxylation of Pro and Ly hydrogen bonds! Packing of collagen molecules Oxidation of lysine and hydroxylysine residues Reactive aldehydes (allysine and hydroxyallysine) form covalent cross-links with neighboring collagen molecules Formation of mature collagen fiber Clinical relevance of collagen Vitamin C deficiency -> defective collagen synthesis -> causes Scurvy Enzyme deficiency or amino acid mutations in collagen cause Ehlers- Danlos syndrome (EDS) connective tissue disorders skin extensibility and fragility and bruise-like discolorations joint hypermobility  Functions/behavior of proteins (other macromolecular complexes) are the result of structural properties Amino acids present, and their sequence == interactions of sidechains and backbone groups in polypeptides Weak interactions (van der Waals, hydrogen bonds, electrostatic interactions, hydrophobic effects) == protein shape and target interactions Changes to structure due to damage, mutation or modification explains the cause of the disease at the molecular level (protein folding; protein dynamics/conformational changes) There is a continual need to convert sequence information into biochemical and biophysical knowledge; to decipher the structural, functional and evolutionary clues encoded in the language of biological sequences How structural biologists revealed the new coronavirus’s structure so quickly – Laura Howes, C&EN (May 2, 2020), Vol 98, Issue17 Credit: Jason McLellan/University of Texas at Austin (spike); H. Tabermann/HZB (protease); Science (polymerase) Structures of SARS-CoV-2's spike protein (left), main protease (middle), and RNA-dependent RNA polymerase (right) have all been solved rapidly by structural biologists around the world.