title: How strong are side chain interactions in the folding intermediate?
abstract: Influence of 12 nonpolar amino acids residues from the hydrophobic core of apomyoglobin on stability of its native state and folding intermediate was studied. Six of the selected residues are from the A, G and H helices; these are conserved in structure of the globin family, although nonfunctional, that is, not involved in heme binding. The rest are nonconserved hydrophobic residues that belong to the B, C, D, and E helices. Each residue was substituted by alanine, and equilibrium pH-induced transitions in apomyoglobin and its mutants were studied by circular dichroism and fluorescent spectroscopy. The obtained results allowed estimating changes in their free energy during formation of the intermediate state. It was first shown that the strength of side chain interactions in the apomyoglobin intermediate state amounts to 15-50% of that in its native state for conserved residues, and practically to 0% for nonconserved residues. These results allow a better understanding of interactions occurring in the intermediate state and shed light on involvement of certain residues in protein folding at different stages.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
authors.forename: Ekaterina N
authors.initials: EN
authors.lastname: Samatova
authors.forename: Natalia S
authors.initials: NS
authors.lastname: Katina
authors.forename: Vitaly A
authors.initials: VA
authors.lastname: Balobanov
authors.forename: Bogdan S
authors.initials: BS
authors.lastname: Melnik
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Dolgikh
authors.forename: Valentina E
authors.initials: VE
authors.lastname: Bychkova
authors.forename: Alexei V
authors.initials: AV
authors.lastname: Finkelstein
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics / Q000502:physiology; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D001059:Apoproteins / Q000737:chemistry* / Q000235:genetics; D009211:Myoglobin / Q000737:chemistry* / Q000235:genetics; D017354:Point Mutation / Q000235:genetics; D011487:Protein Conformation; D017510:Protein Folding; D050661:Sperm Whale; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D001059:Apoproteins; D009211:Myoglobin; C010857:apomyoglobin
references.citation: Nature. 1990 Aug 2;346(6283):440-5
references.pmid: 2377205
references.citation: Anal Biochem. 1974 Oct;61(2):623-7
references.pmid: 4371472
references.citation: Biophys J. 1999 Oct;77(4):2153-74
references.pmid: 10512835
references.citation: J Biol Chem. 1985 Nov 15;260(26):14070-82
references.pmid: 4055771
references.citation: Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2007-12
references.pmid: 10051585
references.citation: Protein Sci. 2005 Oct;14(10):2658-67
references.pmid: 16155199
references.citation: Proc Natl Acad Sci U S A. 2001 May 22;98(11):6127-31
references.pmid: 11353859
references.citation: J Mol Biol. 1988 Jul 5;202(1):127-38
references.pmid: 3172208
references.citation: Annu Rev Biochem. 1993;62:653-83
references.pmid: 8352599
references.citation: Nat Struct Biol. 1998 Feb;5(2):148-55
references.pmid: 9461081
references.citation: Methods Enzymol. 1986;131:266-80
references.pmid: 3773761
references.citation: Mol Biol (Mosk). 2005 Nov-Dec;39(6):1032-41
references.pmid: 16358740
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4765-70
references.pmid: 15769860
references.citation: J Mol Biol. 1999 Aug 20;291(3):671-82
references.pmid: 10448045
references.citation: Biochemistry. 1991 Apr 30;30(17):4113-8
references.pmid: 2021603
references.citation: Science. 1990 Sep 28;249(4976):1544-8
references.pmid: 2218495
references.citation: Nat Struct Biol. 1996 May;3(5):439-45
references.pmid: 8612074
references.citation: Curr Opin Struct Biol. 1995 Feb;5(1):74-8
references.pmid: 7773749
references.citation: Biopolymers. 1989 Oct;28(10):1681-94
references.pmid: 2597724
references.citation: Adv Protein Chem. 2000;53:209-82
references.pmid: 10751946
references.citation: Annu Rev Biochem. 1990;59:631-60
references.pmid: 2197986
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12514-9
references.pmid: 15314218
references.citation: Biochemistry (Mosc). 2008 Jun;73(6):693-701
references.pmid: 18620536
references.citation: J Mol Biol. 2006 Jan 6;355(1):139-56
references.pmid: 16300787
references.citation: J Biol Chem. 1965 Jan;240:299-303
references.pmid: 14253427
references.citation: Eur Biophys J. 1994;23(4):297-305
references.pmid: 7805629
references.citation: Biochemistry. 1993 Apr 13;32(14):3790-6
references.pmid: 8466917
references.citation: J Mol Biol. 1990 Aug 20;214(4):803-5
references.pmid: 2388268
references.citation: Mol Biol (Mosk). 2005 Mar-Apr;39(2):330-5
references.pmid: 15856957
references.citation: Biopolymers. 1989 Oct;28(10):1667-80
references.pmid: 2597723
references.citation: Curr Opin Struct Biol. 1997 Feb;7(1):15-28
references.pmid: 9032062
references.citation: Science. 1993 Nov 5;262(5135):892-6
references.pmid: 8235610
references.citation: J Mol Biol. 1994 Jan 28;235(4):1318-25
references.pmid: 8308894
references.citation: FEBS Lett. 1993 Jun 28;325(1-2):5-16
references.pmid: 8513892
references.citation: Biochemistry. 1998 May 26;37(21):7859-68
references.pmid: 9601047
references.citation: J Mol Biol. 1996 Nov 8;263(4):531-8
references.pmid: 8918936
references.citation: Curr Opin Biotechnol. 1997 Aug;8(4):400-10
references.pmid: 9273848
references.citation: Adv Protein Chem. 1995;47:83-229
references.pmid: 8561052
references.citation: Nat Struct Biol. 1997 Nov;4(11):925-30
references.pmid: 9360609
references.citation: J Biomol NMR. 1995 Nov;6(3):271-6
references.pmid: 8520219
references.citation: Biochemistry (Mosc). 1998 Mar;63(3):294-302
references.pmid: 9526126
references.citation: Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11299-304
references.pmid: 10500171
references.citation: Proteins. 1996 Jul;25(3):267-85
references.pmid: 8844864