title: Mapping polymerization and allostery of hemoglobin S using point mutations.
abstract: Hemoglobin is a complex system that undergoes conformational changes in response to oxygen, allosteric effectors, mutations, and environmental changes. Here, we study allostery and polymerization of hemoglobin and its variants by application of two previously described methods: (i) AllosMod for simulating allostery dynamics given two allosterically related input structures and (ii) a machine-learning method for dynamics- and structure-based prediction of the mutation impact on allostery (Weinkam et al. J. Mol. Biol. 2013, 425, 647-661), now applicable to systems with multiple coupled binding sites, such as hemoglobin. First, we predict the relative stabilities of substates and microstates of hemoglobin, which are determined primarily by entropy within our model. Next, we predict the impact of 866 annotated mutations on hemoglobin's oxygen binding equilibrium. We then discuss a subset of 30 mutations that occur in the presence of the sickle cell mutation and whose effects on polymerization have been measured. Seven of these HbS mutations occur in three predicted druggable binding pockets that might be exploited to directly inhibit polymerization; one of these binding pockets is not apparent in the crystal structure, but only in structures generated by AllosMod. For the 30 mutations, we predict that mutation-induced conformational changes within a single tetramer tend not to significantly impact polymerization; instead, these mutations more likely impact polymerization by directly perturbing a polymerization interface. Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation.
authors: Department of Bioengineering and Therapeutic Sciences, ‡Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California 94158, United States.
authors: Patrick
authors: P
authors: Weinkam
authors: Andrej
authors: A
authors: Sali
mesh_terms: D019794:2,3-Diphosphoglycerate / Q000737:chemistry / Q000378:metabolism; D000494:Allosteric Regulation; D001665:Binding Sites; D019277:Entropy; D006451:Hemoglobin, Sickle / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D017354:Point Mutation; D058105:Polymerization; D011485:Protein Binding; D017434:Protein Structure, Tertiary
chemical_list: D006451:Hemoglobin, Sickle; D019794:2,3-Diphosphoglycerate; D010100:Oxygen
references: Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):118-23
references: 18172203
references: Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5608-13
references: 21415366
references: Protein Sci. 2000 Jan;9(1):10-9
references: 10739242
references: Science. 1991 Dec 13;254(5038):1598-603
references: 1749933
references: Acc Chem Res. 2010 May 18;43(5):652-60
references: 20143816
references: Trends Biochem Sci. 2003 Jul;28(7):361-8
references: 12878003
references: Nat Commun. 2010 Nov 02;1:104
references: 21045822
references: Proteins. 2011 Oct;79(10):2861-70
references: 21905111
references: Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12401-6
references: 16116080
references: Science. 2008 Dec 19;322(5909):1839-42
references: 19056937
references: Biochemistry. 1990 Aug 7;29(31):7133-55
references: 2207096
references: Nature. 1976 Mar 18;260(5548):219-21
references: 1256560
references: J Clin Invest. 1984 Aug;74(2):652-6
references: 6205021
references: Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3504-9
references: 21307307
references: J Mol Biol. 2003 Oct 10;333(1):153-68
references: 14516750
references: Proc Natl Acad Sci U S A. 1978 Apr;75(4):1994-7
references: 347452
references: J Phys Chem B. 2009 Jul 2;113(26):8800-12
references: 19453123
references: Proc Natl Acad Sci U S A. 1983 Dec;80(23):7055-9
references: 6580628
references: Lancet. 1970 Feb 14;1(7642):319-21
references: 4189578
references: Nat Struct Mol Biol. 2006 Sep;13(9):831-8
references: 16906160
references: Biochemistry. 2009 Mar 24;48(11):2394-402
references: 19199810
references: J Mol Biol. 2013 Feb 8;425(3):647-61
references: 23228330
references: Nature. 1980 Feb 28;283(5750):832-4
references: 7360228
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D663-9
references: 21051350
references: Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17674-9
references: 17968016
references: BMC Bioinformatics. 2009 Jun 02;10:168
references: 19486540
references: J Mol Recognit. 2004 Sep-Oct;17(5):497-504
references: 15362110
references: Science. 1949 Nov 25;110(2865):543-8
references: 15395398
references: Protein Sci. 2007 Sep;16(9):1946-56
references: 17660254
references: Protein Sci. 2008 Aug;17(8):1295-307
references: 18560010
references: Proteins. 2009 May 1;75(2):430-41
references: 18837035
references: J Comput Chem. 2007 Jun;28(8):1400-10
references: 17330878
references: Bioinformatics. 2011 Dec 1;27(23):3276-85
references: 21967761
references: J Phys Chem B. 2012 Sep 13;116(36):11004-9
references: 22838506
references: Protein Sci. 1997 Feb;6(2):484-9
references: 9041656
references: J Mol Biol. 1997 Sep 26;272(3):398-407
references: 9325099
references: J Mol Biol. 1982 Jun 25;158(2):251-73
references: 7120411
references: Hemoglobin. 2005;29(2):91-106
references: 15921161
references: Nat Genet. 2011 Mar 20;43(4):295-301
references: 21423179
references: Biophys Chem. 2002 Jul 10;98(1-2):149-64
references: 12128196
references: ChemMedChem. 2011 Jan 3;6(1):153-68
references: 21108295
references: Biochemistry. 1969 Jun;8(6):2567-71
references: 5799137
references: Acta Crystallogr D Biol Crystallogr. 2011 Nov;67(Pt 11):920-8
references: 22101818
references: Clin Chem. 1983 Jan;29(1):110-4
references: 6848245
references: Biophys J. 2005 Feb;88(2):1371-6
references: 15542552
references: Biochemistry. 1966 Jan;5(1):365-85
references: 5938952
references: J Mol Biol. 1996 May 3;258(2):393-410
references: 8627633
references: Protein Sci. 1994 Aug;3(8):1206-12
references: 7987215
references: Biochemistry. 2006 Mar 7;45(9):2820-35
references: 16503637
references: Proc Natl Acad Sci U S A. 1986 Dec;83(24):9363-7
references: 3467311
references: J Mol Biol. 1972 Dec 14;72(1):163-97
references: 4648112
references: Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4134-9
references: 22388747
references: Biophys J. 1978 Jul;23(1):129-45
references: 667302
references: J Mol Biol. 2003 Mar 14;327(1):31-45
references: 12614606
references: Biochemistry. 1995 Apr 25;34(16):5303-8
references: 7727391
references: J Biol Chem. 1979 Sep 10;254(17):8169-72
references: 468817
references: Nature. 1970 Nov 21;228(5273):726-39
references: 5528785
references: J Am Chem Soc. 2012 Feb 22;134(7):3461-71
references: 22263778
references: Proc Natl Acad Sci U S A. 2006 May 16;103(20):7649-54
references: 16684887
references: Blood. 2012 Jun 14;119(24):5671-3
references: 22547579
references: Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):586-91
references: 16407126
references: J Mol Biol. 1996 Dec 13;264(4):743-56
references: 8980683
references: News Physiol Sci. 2001 Aug;16:171-3
references: 11479367
references: J Chem Inf Model. 2009 Nov;49(11):2512-27
references: 19845314
references: Biotechnol Appl Biochem. 1999 Apr;29(2):165-84
references: 10075913
references: PLoS Comput Biol. 2010 May 06;6(5):e1000774
references: 20463873
references: J Mol Biol. 1965 May;12:88-118
references: 14343300
references: Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4875-80
references: 22403063
references: Proteins. 2008 Mar;70(4):1235-42
references: 17853448
references: Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11681-6
references: 22753506
references: J Mol Biol. 1983 Dec 25;171(4):489-559
references: 6663623
references: Nature. 1977 Oct 27;269(5631):772-5
references: 927499