title: Folding intermediate and folding nucleus for I-->N and U-->I-->N transitions in apomyoglobin: contributions by conserved and nonconserved residues.
abstract: Kinetic investigation on the wild-type apomyoglobin and its 12 mutants with substitutions of hydrophobic residues by Ala was performed using stopped-flow fluorescence. Characteristics of the kinetic intermediate I and the folding nucleus were derived solely from kinetic data, namely, the slow-phase folding rate constants and the burst-phase amplitudes of Trp fluorescence intensity. This allowed us to pioneer the phi-analysis for apomyoglobin. As shown, these mutations drastically destabilized the native state N and produced minor (for conserved residues of G, H helices) or even negligible (for nonconserved residues of B, C, D, E helices) destabilizing effect on the state I. On the other hand, conserved residues of A, G, H helices made a smaller contribution to stability of the folding nucleus at the rate-limiting I-->N transition than nonconserved residues of B, D, E helices. Thus, conserved side chains of the A-, G-, H-residues become involved in the folding nucleus before crossing the main barrier, whereas nonconserved side chains of the B-, D-, E-residues join the nucleus in the course of the I-->N transition.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Moscow, Russian Federation.
authors.forename: Ekaterina N
authors.initials: EN
authors.lastname: Samatova
authors.forename: Bogdan S
authors.initials: BS
authors.lastname: Melnik
authors.forename: Vitaly A
authors.initials: VA
authors.lastname: Balobanov
authors.forename: Natalya S
authors.initials: NS
authors.lastname: Katina
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Dolgikh
authors.forename: Gennady V
authors.initials: GV
authors.lastname: Semisotnov
authors.forename: Alexei V
authors.initials: AV
authors.lastname: Finkelstein
authors.forename: Valentina E
authors.initials: VE
authors.lastname: Bychkova
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001059:Apoproteins / Q000737:chemistry* / Q000378:metabolism*; D017124:Conserved Sequence; D006863:Hydrogen-Ion Concentration / Q000187:drug effects; D007700:Kinetics; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009211:Myoglobin / Q000737:chemistry* / Q000378:metabolism*; D011489:Protein Denaturation / Q000187:drug effects; D017510:Protein Folding / Q000187:drug effects; D017433:Protein Structure, Secondary; D050661:Sperm Whale; D013816:Thermodynamics; D014508:Urea / Q000494:pharmacology
chemical_list: D001059:Apoproteins; D050505:Mutant Proteins; D009211:Myoglobin; C010857:apomyoglobin; D014508:Urea
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