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Yawen Bai, Ph.D.

Selected Publications

1)  Hong J, Feng H, Wang F, Ranjan A, Chen J, Jiang J, Ghirlando R, Xiao TS, Wu C, Bai Y.
The Catalytic Subunit of the SWR1 Remodeler Is a Histone Chaperone for the H2A.Z-H2B Dimer.
Mol. Cell. 53: 498-505, 2014.
2)  Kato H, Zhou BR, Feng H, Bai Y.
An evolving tail of centromere histone variant CENP-A.
Cell Cycle. 12: 3133-4, 2013.
3)  Zhou BR, Feng H, Kato H, Dai L, Yang Y, Zhou Y, Bai Y.
Structural insights into the histone H1-nucleosome complex.
Proc. Natl. Acad. Sci. U.S.A. 110: 19390-5, 2013.
4)  Kato H, Jiang J, Zhou B, Rozendaal M, Feng H, Ghirlando R, Xiao T, Straight A, Bai Y.
A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C.
Science. 340: 111--3, 2013.
5)  Hong J, Feng H, Zhou Z, Ghirlando R, Bai Y.
Identification of functionally conserved regions in the structure of the chaperone/CenH3/H4 complex.
J. Mol. Biol. 425: 536-45, 2013.
6)  Zhou BR, Feng H, Ghirlando R, Kato H, Gruschus J, Bai Y.
Histone H4 K16Q mutation, an acetylation mimic, causes structural disorder of its N-terminal basic patch in the nucleosome.
J. Mol. Biol. 421: 30-7, 2012.
7)  Chu X, Wang Y, Gan L, Bai Y, Han W, Wang E, Wang J.
Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B.
PLoS Comput. Biol. 8: e1002608, 2012.
8)  Kato H, van Ingen H, Zhou B, Feng H, Bustin M, Kay LE, Bai Y.
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR.
Proc. Natl. Acad. Sci. U.S.A. 108: 12283-8, 2011.
9)  Bai Y, Zhou Z, Feng H, Zhou B.
Recognition of centromeric histone variant CenH3s by their chaperones-Structurally conserved or not.
Cell Cycle. 10: 3217-3218, 2011.
10)  Zhou Z, Feng H, Zhou B, Ghirlando R, Hu K, Zwolak A, Jenkins LM, Xiao H, Tjandra N, Wu C, Bai Y.
Structural basis for recognition of centromeric histone variant CenH3 by the Scm3 chaperone.
Nature. 472: 234-237, 2011.
Full Text Article. [Journal]
11)  Feng H, Zhou Z, Zhou B, Bai Y.
Structure of the budding yeast Saccharomyces cerevisiae centromeric histones Cse4-H4 complexed with the chaperone Scm3.
Proc Natl Acad Sci U S A. 108: E596, 2011.
12)  Hansen DF, Zhou Z, Feng H, Miller Jenkins LM, Bai Y, Kay LE.
Binding kinetics of histone chaperone Chz1 and variant histone H2A.Z-H2B by relaxation dispersion NMR spectroscopy.
J. Mol. Biol. 387: 1-9, 2009.
13)  Kato H, Gruschus J, Ghirlando R, Tjandra N, Bai Y.
Characterization of the N-terminal domain of histone H3 in condensed nucleosome arrays by hydrogen exchange and NMR.
J Am Chem Soc. 131: 15104-5, 2009.
14)  Hansen DF, Feng H, Zhou Z, Bai Y, Kay L.
Selective characterization of microsecond motions in proteins by NMR relaxation.
J Am Chem Soc. 131: 16257-65, 2009.
15)  Feng H, Jenkins LM, Durell SR, Hayashi R, Mazur SJ, Cherry S, Tropea JE, Miller M, Wlodawer A, Appella E, Bai Y.
Structural basis for p300 Taz2-p53 TAD1 binding and modulation by phosphorylation.
Structure. 17: 202-10, 2009.
16)  Bai Y.
Hydrogen exchange experiments: Detection and characterization of protein folding intermediates. In: Protein Folding, Misfolding, and Aggregation: Classical Themes and Novel Approaches.
London: RSC Biomolecular Sciences; 2008. p. 302 pp. [Book Chapter]
17)  Tu C, Tan YH, Shaw G, Zhou Z, Bai Y, Luo R, Ji X.
Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 angstroms resolution.
Acta Crystallogr. D Biol. Crystallogr. 64: 471-7, 2008.
18)  Zhou Z, Feng H, Hansen D, Kato H, Luk E, Freedberg D, Kay L, Wu C, Bai Y.
NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B.
Nat. Struct. Mol. Biol. 15: 868-9, 2008.
19)  Zhou Z, Feng H, Ghirlando R, Bai Y.
The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H.
J. Mol. Biol. 384: 531-9, 2008.
20)  Hansen DF, Yang D, Feng H, Zhou Z, Wiesner S, Bai Y, Kay LE.
An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange.
J. Am. Chem. Soc. 129: 11468-79, 2007.
21)  Luk E, Vu ND, Patteson K, Mizuguchi G, Wu WH, Ranjan A, Backus J, Sen S, Lewis M, Bai Y, Wu C.
Chz1, a nuclear chaperone for histone H2AZ.
Mol. Cell. 25: 357-68, 2007.
22)  Pokorski JK, Jenkins LM, Feng H, Durell SR, Bai Y, Appella DH.
Introduction of a triazole amino acid into a peptoid oligomer induces turn formation in aqueous solution.
Org. Lett. 9: 2381-3, 2007.
23)  Bai Y, Feng H, Zhou Z.
Population and structure determination of hidden folding intermediates by native-state hydrogen exchange-directed protein engineering and nuclear magnetic resonance.
Methods Mol. Biol. 350: 69-81, 2007.
24)  Wang T, Zhou Z, Bunagan MR, Du D, Bai Y, Gai F.
Probing the folding intermediate of Rd-apocyt b562 by protein engineering and infrared T-jump.
Protein Sci. 2007.
25)  Zhou Z, Bai Y.
Structural biology: analysis of protein-folding cooperativity.
Nature. 445: E16-7; discussion E17-8, 2007.
26)  Kato H, Vu ND, Feng H, Zhou Z, Bai Y.
The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate.
J. Mol. Biol. 365: 881-91, 2007.
27)  Kato H, Feng H, Bai Y.
The folding pathway of T4 lysozyme: the high-resolution structure and folding of a hidden intermediate.
J. Mol. Biol. 365: 870-80, 2007.
28)  Ai X, Zhou Z, Bai Y, Choy WY.
15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions.
J. Am. Chem. Soc. 128: 3916-7, 2006.
29)  Zhou Z, Feng H, Bai Y.
Detection of a hidden folding intermediate in the focal adhesion target domain: Implications for its folding and function.
Proteins. 65: 259-265, 2006.
30)  Yamaguchi H, Durell SR, Feng H, Bai Y, Anderson CW, Appella E.
Development of a substrate-based cyclic phosphopeptide inhibitor of protein phosphatase 2Cdelta, Wip1.
Biochemistry. 45: 13193-202, 2006.
31)  Bai Y.
Folding barriers, cooperativity, and hidden intermediates in small proteins.
Biochem Biophys Res. Commun. 340: 976-983, 2006.
32)  Korzhnev DM, Bezsonova I, Evanics F, Taulier N, Zhou Z, Bai Y, Chalikian TV, Prosser RS, Kay LE.
Probing the Transition State Ensemble of a Protein Folding Reaction by Pressure-Dependent NMR Relaxation Dispersion.
J. Am. Chem. Soc. 128: 5262-5269, 2006.
33)  Bai Y.
Protein folding pathways studied by pulsed- and native-state hydrogen exchange.
Chem Rev. 128: 5262-5269, 2006.
34)  Feng H, Zhou Z, Bai Y.
A protein folding pathway with multiple intermediates at atomic resolution.
Proc Natl Acad Sci USA. 102: 5026-31, 2005.
35)  Choy WY, Zhou Z, Bai Y, Kay LE.
An 15N NMR spin relaxation dispersion study of the folding of a pair of engineered mutants of apocytochrome b562.
J Am Chem Soc. 127: 5066-72, 2005.
36)  Zhou Z, Huang Y, Bai Y.
An on-pathway hidden intermediate and the early rate-limiting transition state of Rd-apocyt b562 characterized by protein engineering.
J Mol Biol. 352: 757, 2005.
37)  Zhou Z, Feng H, Zhou H, Zhou Y, Bai Y.
Design and folding of an engineered multi-domain protein.
Biochemistry. 44: 12107, 2005.
38)  Feng H, Vu ND, Bai Y.
Detection of a hidden folding intermediate of the third domain of PDZ.
J Mol Biol. 346: 345-53, 2005.
39)  Maxwell KL, Wildes D, Zarrine-Afsar A, De Los Rios MA, Brown AG, Friel CT, Hedberg L, Horng JC, Bona D, Miller EJ, Vallée-Bélisle A, Main ER, Bemporad F, Qiu L, Teilum K, Vu ND, Edwards AM, Ruczinski I, Poulsen FM, Kragelund BB, Michnick SW, Chiti F, Bai Y, Hagen SJ, Serrano L, Oliveberg M, Raleigh DP, Wittung-Stafshede P, Radford SE, Jackson SE, Sosnick TR, Marqusee S, Davidson AR, Plaxco KW.
Protein folding: defining a 'standard' set of experimental conditions and a preliminary kinetic data set of two-state proteins.
Protein Sci. 14: 602-16, 2005.
40)  Bai Y, Zhou H, Zhou Y.
Critical nucleation size in the folding of small apparently two-state proteins.
Protein Sci. 13: 1173-81, 2004.
41)  Feng H, Vu ND, Bai Y.
Detection and structure determination of an equilibrium unfolding intermediate of Rd-apocytochrome b562: Native fold with non-native hydrophobic interactions.
J Mol Biol. 343: 1477-85, 2004.
42)  Feng H, Bai Y.
Repacking of hydrophobic residues in a stable mutant of apocytochrome b562 selected by phage display and proteolysis.
Proteins. 56: 426-9, 2004.
43)  Bai Y, Feng H.
Selection of stably folded proteins by phage display with proteolysis.
Eur J Biochem. 271: 1609-14, 2004.
44)  Feng H, Vu ND, Zhou Z, Bai Y.
Structural examination of phi-value analysis in protein folding.
Biochemistry. 43: 14325-31, 2004.
45)  Vu ND, Feng H, Bai Y.
The folding pathway of barnase: the rate-limiting transition state and hidden intermediate under native conditions.
Biochemistry. 43: 3346-56, 2004.
46)  Bai Y.
Hidden intermediates and levinthal paradox in the folding of small proteins.
Biochem Biophys Res Commun. 305: 785-8, 2003.
47)  Feng H, Takei J, Lipsitz R, Tjandra N, Bai Y.
Specific non-native hydrophobic interactions in a hidden intermediate: implications for protein folding (accelerated publication).
Biochemistry. 42: 12461-5, 2003.
48)  Chu RA, Bai Y.
Lack of definable nucleation sites in the rate-limiting transition state of barnase under native conditions.
J Mol Biol. 315: 759-70, 2002.
49)  Takei J, Pei W, Vu D, Bai Y.
Populating partially unfolded forms by hydrogen exchange-directed protein engineering.
Biochemistry. 41: 12308-12, 2002.
50)  Chu R, Takei J, Knowlton JR, Andrykovitch M, Pei W, Kajava AV, Steinbach PJ, Ji X, Bai Y.
Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallography.
J Mol Biol. 323: 253-62, 2002.
51)  Chu R, Pei W, Takei J, Bai Y.
Relationship between the native-state hydrogen exchange and the folding pathway of a four-helix bundle protein.
Biochemistry. 41: 7998-8003, 2002.
52)  Bai Y, Chung J, Dyson HJ, Wright PE.
Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under nondenaturing conditions.
Protein Sci. 10: 1056-66, 2001.
53)  Takei J, Chu RA, Bai Y.
Absence of stable intermediates on the folding pathway of barnase.
Proc Natl Acad Sci USA. 97: 10796-801, 2000.
54)  Bai Y.
Equilibrium amide hydrogen exchange and protein folding kinetics.
J Biomol NMR. 15: 65-70, 1999.
55)  Nawrocki JP, Chu RA, Pannell LK, Bai Y.
Intermolecular aggregations are responsible for the slow kinetics observed in the folding of cytochrome c at neutral pH.
J Mol Biol. 293: 991-5, 1999.
56)  Bai Y.
Kinetic evidence for an on-pathway intermediate in the folding of cytochrome c.
Proc. Natl. Acad. Sci. USA. 96: 477-80, 1999.
57)  Chu RA, Takei J, Barchi JJ, Bai Y.
The relationship between the native-state hydrogen exchange and the folding pathway of barnase.
Biochemistry. 38: 14119-24, 1999.
58)  Englander SW, Sosnick TR, Mayne LC, Shtilerman M, Bai Y.
Fast and slow folding in cytochrome c.
Acc Chem Res. 31: 737-44, 1998.
59)  Bai Y, Karimi A, Dyson HJ, Wright PE.
Absence of a stable intermediate on the folding pathway of protein A.
Protein Sci. 6: 1449-57, 1997.
60)  Englander SW, Mayne L, Bai Y, Sosnick TR.
Hydrogen exchange and protein folding: the modern legacy of Linderstrom-Lang.
Protein Sci. 6: 1101-9, 1997.
61)  Bai Y, Englander SW.
Future directions in protein folding: the multi-state nature of protein structure.
Proteins. 24: 145-51, 1996.
62)  Bai Y, Sosnick TR, Mayne L, Englander SW.
Protein folding intermediates: native-state hydrogen exchange.
Science. 269: 192-7, 1995.
63)  Bai Y, Englander JJ, Mayne L, Milne JS, Englander SW.
Thermodynamic parameters from hydrogen exchange measurements.
Methods Enzymol. 259: 344-56, 1995.
64)  Bai Y, Englander SW.
Hydrogen bond strength and beta-sheet propensities: The role of a side chain blocking effect.
Proteins: Struct Funct Genet. 18: 262-6, 1994.
65)  Bai Y, Milne JS, Mayne L, Englander SW.
Protein stability parameters measured by hydrogen exchange.
Proteins. 20: 4-14, 1994.
66)  Zhou H, Hull LA, Kallenbach NR, Mayne L, Bai Y, Englander SW.
Quantitative evaluation of stabilizing interactions in a prenucleated alpha-helix by hydrogen exchange.
J Am Chem Soc. 116: 6482-3, 1994.
67)  Connelly GP, Bai Y, Jeng MF, Englander SW.
Isotopic effects in peptide group hydrogen exchange.
Proteins. 17: 87-92, 1993.
68)  Bai Y, Milne JS, Mayne L, Englander SW.
Primary structure effects on peptide group exchange.
Proteins. 17: 87-92, 1993.
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This page was last updated on 2/14/2014.