Quaternary Structure of Proteins: Stability and Function through Subunit Assembly, Study notes of Construction

Download Quaternary Structure of Proteins: Stability and Function through Subunit Assembly and more Study notes Construction in PDF only on Docsity! Quaternary structure • Assembly of multiple polypeptide chains in one integral structure • The arrangement of the subunits gives rise to a stable structure • Subunits may be identical or different • A common shorthand for describing such proteins is to use Greek letters for each type of subunit, and subscript numeral to specify numbers of units. – A protein designated α2βγ consists of two α units and one each of β and γ Petsko and Ringe 1 = monomer 2 = dimer 3 = trimer 4 = tetramer 5 = pentamer 6 = hexamer 7 = heptamer 8 = octamer 9 = nonamer 10 = decamer 11 = undecamer 12 = dodecamer • Quaternary structure adds stability by decreasing the surface/volume ratio of smaller subunit • Simplifies the construction of large complexes – viral capsids are often composed of multiples of 60 proteins – 20s subunit of proteosomes contain four heptameric rings (4 x 7 = 28 subunits) Hepatitis B virus proteosome degrades unfolded protein—cellular garbage disposal Escher Human immunodeficiency virus aspartyl protease Most protein multimers have significant rotational symmetry in the placement of the subunits Potassium channel Chemistry Nobel prize, 2003 Arrangement of subunits Advantages of building protein complexes • Easier to evolve—shorter genes • Easier to transcribe and translate—quicker response • Robust against error in transcription/translation (1 in 2000 amino acids) • Additional layer of regulation – Allosteric properties not present in monomer – Many multiprotein complexes regulate their physiological function through conformational changes – Changes in quaternary structure can occur through conformational changes within individual subunits or through reorientation of the subunits relative to each other. Hemoglobin v. myoglobin Hemoglobin: heterodimer of dimer (α2β2) Oxygen binding in hemoglobin is highly cooperative cooperativity is achieved through domain rotation compare with myoglobin, which is a monomeric protein Eaton et al, NSB 6, 351 (1999) E. coli RNA polymerase dimer The N terminal domain (NTD) is thought to be involved in dimer formation The interface consists of both polar (E32, T38, S50, and Q227) and hydrophobic (F35, F8, L31, L39, I46) residues, which together form a cluster that provides more stability than a single pair of polar–polar or hydrophobic–hydrophobic interaction Kannan et al, Protein Sci 10, 46 (2001) 3D domain swapping • A common mechanism for forming oligomeric proteins from monomers • Creates an interface between different polypeptide chains which is identical to that seen within the monomer • The interface for dimerization has already been evolved and optimized • Monomers may exchange a secondary structural element (strand or helix) or an entire domain Bennett et al. Structure 14, 811 (2006) • Engineer monomeric staphylococcal nuclease into a dimer • Deletion creates steric clash involving side chains and promotes dimerization Altering quaternary structure ultracentrifugation MW: 16 kDa x 2 = 32 kDa Green et al, NSB 2, 746 (1995) Strand exchange Natural proteins often dimerize by exchanging a strand or a helix Domain-swapped structures are biologically significant In p13suc1, the hinge loop works as a loaded molecular spring Mutation in the hinge loop shifts the monomer-dimer equilibrium The binding of a ligand (e.g. phosphate and phosphopeptide) also shifts the equilibrium in wild type by altering the dynamic properties of the native state ensemble Schymkowitz et al, NSB 8, 888 (2001) p13suc1 hinge loop Domain swapped protein fibrils may be involved in diseases prion, hereditary hemorrhagic stroke disorder prion disease mutations map to domain swapping helix consecutive domain swapping is also possible leading to fibril formation Bennett et al. Structure 14, 811 (2006)Knaus et al, NSB 8, 770 (2001) prion dimer Deposition diseases Deposition diseases are “conformation” diseases characterized by aggregation of native proteins –Amyloidic : ordered fibril like deposits of proteins »Alzheimer’s, Parkinson’s, Huntington, Type II diabetes »beta strands running perpendicular to the fibril axis –Non-amyloidic fibrils or aggregates »sick cell anemia »serpinopathies The proteins implicated in these diseases usually perform well- characterized, essential biological functions under normal circumstances … until things fall apart A change in environment or genetic predisposition exposes a protein for the growth of aggregates—unintended quaternary structure