Buyong Ma, Ph.D.
School of Pharmacy, Shanghai Jiaotong University.
E-mail: mabuyong@sjtu.edu.cn

Professional Career
2020 Professor | School of Pharmacy, Shanghai Jiaotong University, China
2003-2020 Senior Scientist | Leidos Biomedical Research, Inc. NCI, Frederick, MD. USA
2002-2003 Scientist | Locus Pharmaceuticals, Inc; Philadelphia, PA, USA.
1998-2002 Research Fellow | Laboratory of Experimental and Computational Biology, CCR, NCI, NIH, Frederick, MD, USA.
1995-1998 Postdoctoral Research Associate | Computational Center for Molecular Structure and Design, University of Georgia, Athens, GA, USA.
Advisor: N. L. Allinger.

Education
1991-1995 Ph.D. in Physical Chemistry | University of Georgia, Athens, GA, USA
Thesis: Computational approach to chemical problems by ab initio quantum mechanical methods. (Advisor: H. F. Schaefer).
1984-1987 M.S. in Polymer Chemistry | Hubei Research Institute of Chemistry, China
1980-1984 B.S. in Chemical Engineering | Hefei University of Technology, China

Research Interest
(1) Computational structural/chemical biology of cancer and protein aggregation diseases, including Alzheimer’s disease, Parkinson’s disease, Prion disease, Systemic light chain amyloidosis.
(2) Computational systems biology, protein interaction and network in cancer and immunology.
(3) Conformational dynamics in protein function.
(4) Computational Antibody/Antigen Design, Protein Engineering.

Research Achievements
More than 190 scientific publications, including more than twenty in PNAS、JACS、Chemical Review, Nature Communication, Nature Structural & Molecular Biology. (1) Established the popular theory of “Conformation selection” in biomolecular recognition, in complementary to traditional “Lock and key”and “Induced Fit”. (2) Delineated structure characteristic of hotspot in protein-protein interaction. (3) Pioneer in computational study of protein aggregation. The first to reveal atomic structure of amyloid.
Google Scholar: https://scholar.google.com/citations?user=6VkxqHIAAAAJ&hl=en
All Since 2015
Citations
17925 7047
h-index
60 42
i10-index
170 123


Editorial Board
Antibodies, Scientifica, Journal of Alzheimer's Disease and Related Diseases, Exploration of Immunology。

Complete publication list
2020
1. Chen, Y. Zhao, J. Nussinov, R. Wei, G. Ma, B. Computational Investigation of Gantenerumab and Crenerzumab’s Recognition of Aβ Fibrils in Alzheimer's Disease Brain Tissue， ACS Chem Neurosci, in revision.
2. Derreumaux, P. et al. When Amyloid Proteins Talk to Each Other: a Joint Experimental/Theoretical Perspective on Alzheimer, Parkinson, Type II Diabetes and Amyotrophic Lateral Sclerosis Diseases, Chem. Rev. in revision.
3. He, Y, Agnihotri, P. Rangarajan,S. Chen, Y. Kerzic, M. Ma, B. Nussinov, R. Mariuzza, R. and Orban, J. Peptide–MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs), J. Mol. Bio. in revision.
2019
4. Luo, H. Hu, L. Ma, B. Zhao, M. Luo, M. Deng, M. Deng, S. Ye, H. Lin, T. Chen, J. Lu, H. Molecular dynamics based improvement of the solubilizing self-cleavable tag Zbasic-ΔI-CM application in the preparation of recombinant proteins in Escherichia coli. Biochemical and biophysical research communications 513 (2), 412-418
5. Lucchesi, C.A., Zhang, J., Ma, B., Chen, M. and Chen, X. Disruption of the Rbm38-eIF4E complex with a synthetic peptide Pep8 increases p53 expression. Cancer Res. 2019 79(4): 807–818.
6. Lei, J., Qi, R., Tang, Y., Wang, W., Wei, G., Nussinov, R. and Ma, B. Conformational stability and dynamics of the cancer-associated isoform Delta133p53beta are modulated by p53 peptides and p53-specific DNA. FASEB J 2019, 33(3): 4225–4235.
7. Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. (2019) Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. Methods Mol Biol, 1851, 317-335.
8. Guven-Maiorov, E. Tsai, CJ. Ma, B. Nussinov, R. Interface-based structural prediction of novel host-pathogen interactions. Computational Methods in Protein Evolution, 2019, 317-335
9. Zhao, J., Nussinov, R. and Ma, B. Antigen binding allosterically promotes Fc receptor recognition. MAbs, 11 (1), 58-74
2018
10. Zhao, J., Zhang, B., Zhu, J., Nussinov, R. and Ma, B. (2018) Structure and energetic basis of overrepresented lambda light chain in systemic light chain amyloidosis patients. BBA Molecular Basis of Desease. doi: 10.1016/j.bbadis.2017.12.009. 1864, 2294-2303
11. Zhang, M. Zheng, J. Nussinov, R. Ma, B. Molecular recognition between Aβ-specific single-domain antibody and Aβ Misfolded aggregates. Antibodies 7 (3), 25
12. Li, X., Dong, X., Wei, G., Margittai, M., Nussinov, R. and Ma, B. (2018) The distinct structural preferences of tau protein repeat domains. Chem Commun (Camb), 54, 5700-5703.
13. Weismiller, H.A., Murphy, R., Wei, G., Ma, B., Nussinov, R. and Margittai, M. (2018) Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms. J Biol Chem, 293, 17336-17348.
14. Rangarajan, S., He, Y., Chen, Y., Kerzic, M.C., Ma, B., Gowthaman, R., Pierce, B.G., Nussinov, R., Mariuzza, R.A. and Orban, J. (2018) Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. J Biol Chem, 293, 15991-16005
15. Qi, R., Wei, G., Ma, B. and Nussinov, R. (2018) Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example. Methods Mol Biol, 1777, 101-119.
16. Ren, B., Hu, R., Zhang, M., Liu, Y., Xu, L., Jiang, B., Ma, J., Ma, B., Nussinov, R. and Zheng, J. (2018) Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies. Methods Mol Biol, 1777, 429-447.
17. Song, N.Y., Zhu, F., Wang, Z., Willette-Brown, J., Xi, S., Sun, Z., Su, L., Wu, X., Ma, B., Nussinov, R. et al. (2018) IKKalpha inactivation promotes Kras-initiated lung adenocarcinoma development through disrupting major redox regulatory pathways. Proc Natl Acad Sci U S A, 115, E812-E821.
18. Qian, Z., Zou, Y., Zhang, Q., Chen, P., Ma, B., Wei, G. and Nussinov, R. (2018) Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition. Biochim Biophys Acta. s0005-2736, 30046-30044.
19. J Zhao, R Nussinov, WJ Wu, B Ma In silico methods in antibody design Antibodies 7 (3), 22
2017
20. Wang, M., Zhu, D., Zhu, J., Nussinov, R. and Ma, B. (2017) Local and global anatomy of antibody-protein antigen recognition. J Mol Recognit. 21, e2693.
21. Zhao, J., Nussinov, R. and Ma, B. (2017) Mechanisms of recognition of Abeta monomer, oligomer, and fibril by homologous antibodies. J Biol Chem, 292, 18325-18343.
22. Dong, X., Sun, Y., Wei, G., Nussinov, R. and Ma, B.* (2017) Binding of protofibrillar Aß trimers to lipid bilayer surface enhances Aß structural stability and causes membrane thinning Phys Chem Chem Phys. 19, 27556-27569.
23. Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. (2017) Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer. J Mol Biol, 429, 3925-3941.
24. Libardo, M.D.J., Bahar, A.A., Ma, B., Fu, R., McCormick, L.E., Zhao, J., McCallum, S.A., Nussinov, R., Ren, D., Angeles-Boza, A.M. et al. (2017) Nuclease Activity Gives an Edge to Host-Defense Peptide Piscidin 3 over Piscidin 1, Rendering it more Effective against Persisters and Biofilms. FEBS J. 284 (21), 3662-3683
25. Zhang, M., Zheng, J., Nussinov, R. and Ma, B. (2017) Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane. Sci Rep, 7, 2635.
26. Xu, L., Ma, B., Nussinov, R. and Thompson, D. (2017) Familial Mutations May Switch Conformational Preferences in alpha-Synuclein Fibrils. ACS Chem Neurosci, 8, 837-849.
27. Zhao, J., Nussinov, R. and Ma, B. (2017) Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Eng Des Sel, 30, 67-76.
28. Gong, Y., Zhu, Y., Zou, Y., Ma, B., Nussinov, R. and Zhang, Q. (2017) Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity. J Phys Chem B, 121, 508-517.
29. Gan, W., Schneidman, D., Zhang, N., Ma, B. and Nussinov, R. (2017) Probing Oligomerized Conformations of Defensin in the Membrane. Methods Mol Biol, 1529, 353-362.
2016
30. Zou, Y., Sun, Y., Zhu, Y., Ma, B., Nussinov, R. and Zhang, Q. (2016) Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein. ACS Chem Neurosci, 7, 286-296.
31. 166. Zhu, Y., Ma, B., Qi, R., Nussinov, R. and Zhang, Q. (2016) Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations. J Phys Chem B, 120, 3551-3559.
32. Zhan, C., Qi, R., Wei, G., Guven-Maiorov, E., Nussinov, R. and Ma, B. (2016) Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization. Protein Eng Des Sel, 29, 347-354.
33. Maximova, T., Moffatt, R., Ma, B., Nussinov, R. and Shehu, A. (2016) Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol, 12, e1004619.
34. Ma, B., Zhao, J. and Nussinov, R. (2016) Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. Biochim Biophys Acta, 1860, 2672-2681.
35. Ma, B. and Nussinov, R. (2016) Protein dynamics: Conformational footprints. Nat Chem Biol, 12, 890-891.
36. Lei, J., Qi, R., Wei, G., Nussinov, R. and Ma, B. (2016) Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant. Phys Chem Chem Phys, 18, 8098-8107.
37. Hewitt, W.M., Lountos, G.T., Zlotkowski, K., Dahlhauser, S.D., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B. et al. (2016) Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Angew Chem Int Ed Engl, 55, 5703-5707.
38. Xu, L., Nussinov, R. and Ma, B. (2016) Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the alpha-synuclein fibrils. Eur J Med Chem, 121, 841-850.
39. Xu, L., Zheng, J., Margittai, M., Nussinov, R. and Ma, B. (2016) How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability? ACS Chem Neurosci, 7, 565-575.
40. Xu, L., Nussinov, R. and Ma, B. (2016) Allosteric stabilization of the amyloid-beta peptide hairpin by the fluctuating N-terminal. Chem Commun (Camb), 52, 1733-1736.
41. Wei, G., Xi, W., Nussinov, R. and Ma, B. (2016) Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev, 116, 6516-6551.
2015
42. Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R. and Ishii, Y. (2015) Abeta(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease. Nat Struct Mol Biol, 22, 499-505.
43. Qi, R., Luo, Y., Wei, G., Nussinov, R. and Ma, B. (2015) Aβ “Stretching-and-Packing” Cross-Seeding Mechanism Can Trigger Tau Protein Aggregation. The Journal of Physical Chemistry Letters, 6, 3276-3282.
44. Zhu, Y., Yang, S., Qi, R., Zou, Y., Ma, B., Nussinov, R. and Zhang, Q. (2015) Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein. J Phys Chem B, 119, 14236-14244.
45. Datta, S.A., Clark, P.K., Fan, L., Ma, B., Harvin, D.P., Sowder, R.C., 2nd, Nussinov, R., Wang, Y.X. and Rein, A. (2015) Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly. J Virol, 90, 1773-1787.
46. Clausen, R., Ma, B., Nussinov, R. and Shehu, A. (2015) Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PLoS Comput Biol, 11, e1004470.
47. Baram, M., Atsmon-Raz, Y., Ma, B., Nussinov, R. and Miller, Y. (2015) Amylin-Abeta oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease. Phys Chem Chem Phys. 18(4): 2330–2338.
48. Xu, L., Shan, S., Chen, Y., Wang, X., Nussinov, R. and Ma, B. (2015) Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Abeta40 Peptide Oligomerization. J Chem Inf Model, 55, 1218-1230.
49. Zhou, P., Zhang, N., Nussinov, R. and Ma, B. (2015) Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. J Comput Biol, 22, 876-886.
50. Fetics, S.K., Guterres, H., Kearney, B.M., Buhrman, G., Ma, B., Nussinov, R. and Mattos, C. (2015) Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. Structure, 23, 505-516.
51. Miller, Y., Ma, B. and Nussinov, R. (2015) Polymorphism in Self-Assembly of Peptide-Based beta-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity. J Phys Chem B, 119, 482-490.
52. Cronin, M., Coolbaugh, M.J., Nellis, D., Zhu, J., Wood, D.W., Nussinov, R. and Ma, B. (2015) Dynamics differentiate between active and inactive inteins. Eur J Med Chem, 91, 51-62.
2014
53. Zhu, Y., Wu, Y., Luo, Y., Zou, Y., Ma, B. and Zhang, Q. (2014) R102Q mutation shifts the salt-bridge network and reduces the structural flexibility of human neuronal calcium sensor-1 protein. J Phys Chem B, 118, 13112-13122.
54. Ma, B., Kolb, S., Diprima, M., Karna, M., Tosato, G., Yang, Q., Huang, Q. and Nussinov, R. (2014) Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors, 32, 236-246.
55. Huang, Q., Yu, L., Levine, A.J., Nussinov, R. and Ma, B. (2014) Dipeptide analysis of p53 mutations and evolution of p53 family proteins. Biochim Biophys Acta, 1844, 198-206.
56. Nussinov, R., Ma, B. and Tsai, C.J. (2014) Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys Chem, 186, 22-30.
57. Ma, B. and Nussinov, R. (2014) Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr Pharm Des, 20, 1293-1301.
58. Qi, R., Luo, Y., Ma, B.*, Nussinov, R. and Wei, G. (2014) Conformational distribution and alpha-helix to beta-sheet transition of human amylin fragment dimer. Biomacromolecules, 15, 122-131.
59. Meyer, V., Dinkel, P.D., Luo, Y., Yu, X., Wei, G., Zheng, J., Eaton, G.R., Ma, B., Nussinov, R., Eaton, S.S. et al. (2014) Single mutations in tau modulate the populations of fibril conformers through seed selection. Angew Chem Int Ed Engl, 53, 1590-1593.
60. Luo, Y., Ma, B., Nussinov, R. and Wei, G. (2014) Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation. J Phys Chem Lett, 5, 3026-3031.
61. Ji, X., Huang, Q., Yu, L., Nussinov, R. and Ma, B. (2014) Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs. Int J Mol Sci, 15, 13275-13298.
62. Hwang, S.Y., Zhang, M., Zhang, C., Ma, B., Zheng, J. and Peng, Z. (2014) Carbon monoxide in controlling the surface formation of Group VIII metal nanoparticles. Chem Commun (Camb), 50, 14013-14016.
63. Dai, D., Huang, Q., Nussinov, R. and Ma, B. (2014) Promiscuous and specific recognition among ephrins and Eph receptors. Biochim Biophys Acta, 1844, 1729-1740.
64. Ji, X., Ma, L., Huang, Q., Li, Z., Zhao, J., Huang, W., Ma, B. and Yu, L. (2014) Network Effect of Wt-Mutant P53 Interactions And Implications on P53 Gene Therapy. Current pharmaceutical design, 20, 1259-1267.
2013
65. Luo, Y., Yu, X., Dinkel, P., Zheng, J., Margittai, M., Nussinov, R., Wei, G. and Ma, B. (2013) Molecular Insights into the Reversible Formation of Tau Protein Fibrils. Chemical Communications, DOI: 10.1039/c3cc00241a.
66. Nussinov, R., Tsai, C.J. and Ma, B. (2013) The underappreciated role of allostery in the cellular network. Annu Rev Biophys, 42, 169-189.
67. Nussinov, R., Ma, B. and Tsai, C.J. (2013) A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. Biochim Biophys Acta, 1834, 820-829.
68. Ma, B. and Nussinov, R. (2013) Structured crowding and its effects on enzyme catalysis. Top Curr Chem, 337, 123-137.
69. Nussinov, R., Ma, B., Tsai, C.J. and Csermely, P. (2013) Allosteric conformational barcodes direct signaling in the cell. Structure, 21, 1509-1521.
70. Xu, Y., Wang, H., Nussinov, R. and Ma, B. (2013) Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics. 13(8):1339-51
71. Yu, X., Luo, Y., Dinkel, P., Zheng, J., Wei, G., Margittai, M., Nussinov, R. and Ma, B. (2012) Cross-seeding and conformational selection between three- and four-repeat human Tau proteins. J Biol Chem, 287, 14950-14959.
2012
72. Xu, Y., Ma, B. and Nussinov, R. (2012) Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP. J Phys Chem B, 16, 4801-4811.
73. Stagno, J.R., Ma, B., Li, J., Altieri, A.S., Byrd, R.A. and Ji, X. (2012) Crystal structure of a plectonemic RNA supercoil. Nat Commun, 3, 901.
74. Siddiqua, A., Luo, Y., Meyer, V., Swanson, M.A., Yu, X., Wei, G., Zheng, J., Eaton, G.R., Ma, B., Nussinov, R. et al. (2012) Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau. J Am Chem Soc, 134, 10271-10278.
75. Nussinov, R. and Ma, B. (2012) Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol, 10, 2.
76. Hu, L., Cui, W., He, Z., Shi, X., Feng, K., Ma, B. and Cai, Y.D. (2012) Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One, 7, e39369.
77. Ma, B. and Nussinov, R. (2012) Selective molecular recognition in amyloid growth and transmission and cross-species barriers. J Mol Biol, 421, 172-184.
2011
78. Ma, B. and Nussinov, R. (2011) Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide. J Biol Chem, 286, 34244-34253.
79. Ma, B., Tsai, C.J., Haliloglu, T. and Nussinov, R. (2011) Dynamic allostery: linkers are not merely flexible. Structure, 19, 907-917.
80. Miller, Y., Ma, B. and Nussinov, R. (2011) Synergistic interactions between repeats in tau protein and Abeta amyloids may be responsible for accelerated aggregation via polymorphic states. Biochemistry, 50, 5172-5181.
81. Yuan, P., Liang, K., Ma, B., Zheng, N., Nussinov, R. and Huang, J. (2011) Multiple-targeting and conformational selection in the estrogen receptor: computation and experiment. Chem Biol Drug Des, 78, 137-149.
82. Parthasarathy, S., Long, F., Miller, Y., Xiao, Y., McElheny, D., Thurber, K., Ma, B., Nussinov, R. and Ishii, Y. (2011) Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's beta by solid-state NMR spectroscopy. J Am Chem Soc, 133, 3390-3400.
83. Miller, Y., Ma, B. and Nussinov, R. (2011) The unique Alzheimer's beta-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions. J Am Chem Soc, 133, 2742-2748.
2010
84. Ma, B. and Nussinov, R. (2010) Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer. J Biol Chem, 285, 37102-37110.
85. Ma, B. and Nussinov, R. (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol, 14, 652-659.
86. Ma, B., Tsai, C.J., Pan, Y. and Nussinov, R. (2010) Why does binding of proteins to DNA or proteins to proteins not necessarily spell function? ACS Chem Biol, 5, 265-272.
87. Miller, Y., Ma, B. and Nussinov, R. (2010) Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A, 107, 9490-9495.
88. Miller, Y., Ma, B. and Nussinov, R. (2010) Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev, 110, 4820-4838.
89. Miller, Y., Ma, B., Tsai, C.J. and Nussinov, R. (2010) Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH. Proc Natl Acad Sci U S A, 107, 14128-14133.
90. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2010) Mechanisms of transcription factor selectivity. Trends Genet, 26, 75-83.
Before 2010
91. Yu, X., Wang, Q., Yang, J.C., Buch, I., Tsai, C.J., Ma, B., Cheng, S.Z., Nussinov, R. and Zheng, J. (2009) Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain. Biomacromolecules, 10, 390-399.
92. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control. Phys Biol, 6, 013001.
93. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci, 34, 594-600.
94. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2009) How do transcription factors select specific binding sites in the genome? Nat Struct Mol Biol, 16, 1118-1120.
95. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci. 34(12):594-600.
96. Miller, Y., Ma, B. and Nussinov, R. (2009) Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys J, 97, 1168-1177.
97. Ma, B. and Nussinov, R. (2009) Regulating highly dynamic unstructured proteins and their coding mRNAs. Genome Biol, 10, 204.
98. Ma, B. and Nussinov, R. (2009) Amplification of signaling via cellular allosteric relay and protein disorder. Proc Natl Acad Sci U S A, 106, 6887-6888.
99. del Sol, A., Tsai, C.J., Ma, B. and Nussinov, R. (2009) The origin of allosteric functional modulation: multiple pre-existing pathways. Structure, 17, 1042-1050.
100. Zheng, J., Ma, B., Chang, Y. and Nussinov, R. (2008) Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association. Front Biosci, 13, 3919-3930.
101. Zheng, J., Jang, H., Ma, B. and Nussinov, R. (2008) Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. J Phys Chem B, 112, 6856-6865.
102. Jang, H., Ma, B., Lal, R. and Nussinov, R. (2008) Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J, 95, 4631-4642.
103. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2008) Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact? Chem Rev, 108, 1225-1244.
104. Ma, B. and Levine, A.J. (2007) Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Nucleic Acids Res, 35, 7733-7747.
105. Ma, B., Pan, Y., Zheng, J., Levine, A.J. and Nussinov, R. (2007) Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res, 35, 2986-3001.
106. Zheng, J., Jang, H., Ma, B., Tsai, C.J. and Nussinov, R. (2007) Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J, 93, 3046-3057.
107. Ma, B. and Nussinov, R. (2007) Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Curr Top Med Chem, 7, 999-1005.
108. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2007) Towards drugs targeting multiple proteins in a systems biology approach. Curr Top Med Chem, 7, 943-951.
109. Jang, H., Ma, B. and Nussinov, R. (2007) Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. BMC Struct Biol, 7, 21.
110. Hu, Z., Bowen, D., Southerland, W.M., del Sol, A., Pan, Y., Nussinov, R. and Ma, B. (2007) Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol, 3, e117.
111. Liu, J., Pan, Y., Ma, B. and Nussinov, R. (2006) "Similarity Trap" in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains. Structure, 14, 1811-1821.
112. Zheng, J., Ma, B. and Nussinov, R. (2006) Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure. Phys Biol, 3, P1-4.
113. Ma, B. and Nussinov, R. (2006) Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol.
114. Jang, H., Ma, B., Woolf, T.B. and Nussinov, R. (2006) Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J, 91, 2848-2859.
115. Zheng, J., Ma, B., Tsai, C.J. and Nussinov, R. (2006) Structural Stability and Dynamics of an Amyloid-forming Peptide GNNQQNY from the Yeast Prion Sup-35. Biophys J.
116. Pan, Y., Ma, B., Levine, A.J. and Nussinov, R. (2006) Comparison of the human and worm p53 structures suggests a way for enhancing stability. Biochemistry, 45, 3925-3933.
117. Ma, B. and Nussinov, R. (2006) The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant. Biophys J, 90, 3365-3374.
118. Wolfson, H.J., Shatsky, M., Schneidman-Duhovny, D., Dror, O., Shulman-Peleg, A., Ma, B. and Nussinov, R. (2005) From structure to function: methods and applications. Curr Protein Pept Sci, 6, 171-183.
119. Pan, Y., Ma, B. and Nussinov, R. (2005) CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible. J Mol Biol, 350, 514-527.
120. Ma, B., Pan, Y., Gunasekaran, K., Keskin, O., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins. Phys Biol, 2, S56-66.
121. Keskin, O., Ma, B., Rogale, K., Gunasekaran, K. and Nussinov, R. (2005) Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol, 2, S24-S35.
122. Ma, B., Pan, Y., Gunasekaran, K., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface. Proc Natl Acad Sci U S A, 102, 3988-3993.
123. Pan, Y., Ma, B., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) In the Quest for Stable Rescuing Mutants of p53: Computational Mutagenesis of Flexible Loop L1. Biochemistry, 44, 1423-1432.
124. Haspel, N., Zanuy, D., Ma, B., Wolfson, H. and Nussinov, R. (2005) A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. J Mol Biol, 345, 1213-1227.
125. Keskin, O., Ma, B. and Nussinov, R. (2005) Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol, 345, 1281-1294.
126. Haliloglu, T., Keskin, O., Ma, B. and Nussinov, R. (2005) How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J, 88, 1552-1559.
127. Ma, B. and Nussinov, R. (2004) From computational quantum chemistry to computational biology: Experiments and computations are (full) partners. Physical Biology, 1, p23-p26.
128. Li, X., Keskin, O., Ma, B., Nussinov, R. and Liang, J. (2004) Protein-Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking. J Mol Biol, 344, 781-795.
129. Zanuy, D., Nurit, H., Tsai, H.H., Ma, B., Gunasekaran, K., Wolfson, H. and Nussinov, R. (2004) Side chain interactions determine the amyloid organization: a single layer ß-sheet molecular structure of the calcitonin peptide segment 15–19. Physical Biology, 1, 89-99.
130. Tsai, H.H., Zanuy, D., Haspel, N., Gunasekaran, K., Ma, B., Tsai, C.J. and Nussinov, R. (2004) The stability and dynamics of the human calcitonin amyloid peptide DFNKF. Biophys J, 87, 146-158.
131. Tsai, H.H., Tsai, C.J., Ma, B. and Nussinov, R. (2004) In silico protein design by combinatorial assembly of protein building blocks. Protein Sci, 13, 2753-2765.
132. Pan, Y., Ma, B., Keskin, O. and Nussinov, R. (2004) Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. J Biol Chem, 279, 30523-30530.
133. Ma, B. and Nussinov, R. (2004) Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. J Biol Chem, 279, 53875-53885.
134. Zanuy, D., Gunasekaran, K., Ma, B., Tsai, H.H., Tsai, C.J. and Nussinov, R. (2004) Insights into amyloid structural formation and assembly through computational approaches. Amyloid, 11, 143-161.
135. Gunasekaran, K., Ma, B. and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins, 57, 433-443.
136. Zanuy, D., Ma, B. and Nussinov, R. (2003) Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J, 84, 1884-1894.
137. Ma, B., Elkayam, T., Wolfson, H. and Nussinov, R. (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A, 100, 5772-5777.
138. Ma, B. and Nussinov, R. (2003) Energy landscape and dynamics of the b-hairpin G peptide and its isomers: Topology and sequences. Protein Sci, 12, 1882-1893.
139. Ma, B. and Nussinov, R. (2003) Molecular dynamics simulations of the unfolding of b2-microglobulin and its variants. Protein Eng, 16, 561-575.
140. Li, W., Ma, B. and Shapiro, B.A. (2003) Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations. Nucleic Acids Research, 31, 629-638.
141. Gunasekaran, K., Ma, B., Ramakrishnan, B., Qasba, P.K. and Nussinov, R. (2003) Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I. Biochemistry, 42, 3674-3687.
142. Gunasekaran, K., Ma, B. and Nussinov, R. (2003) Triggering loops and enzyme function: identification of loops that trigger and modulate movements. J Mol Biol, 332, 143-159.
143. Sham, Y.Y., Ma, B., Tsai, C.J. and Nussinov, R. (2002) Thermal unfolding molecular dynamics simulation of E-coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway. Proteins, 46, 308-320.
144. Ma, B., Shatsky, M., Wolfson, H.J. and Nussinov, R. (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci, 11, 184-197.
145. Ma, B. and Nussinov, R. (2002) Molecular dynamics simulations of alanine rich b-sheet oligomers: Insight into amyloid formation. Protein Sci, 11, 2335-2350.
146. Ma, B. and Nussinov, R. (2002) Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Ab16-22, Ab16-35, and Ab10-35): Sequence effects. Proc Natl Acad Sci U S A, 99, 14126-14131.
147. Halperin, I., Ma, B., Wolfson, H. and Nussinov, R. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
148. Tsai, C.J., Ma, B., Sham, Y.Y., Kumar, S., Wolfson, H. and Nussinov, R. (2001) A hierarchical, building blocks based computational method for protein structure prediction. IBM Journal of Research and Development, Issue on life Science., 45.
149. Tsai, C.J., Ma, B., Sham, Y.Y., Kumar, S. and Nussinov, R. (2001) Structured disorder and conformational selection. Proteins, 44, 418-427.
150. Tsai, C.D., Ma, B., Kumar, S., Wolfson, H. and Nussinov, R. (2001) Protein folding: binding of conformationally fluctuating building blocks via population selection. Crit Rev Biochem Mol Biol, 36, 399-433.
151. Sham, Y.Y., Ma, B., Tsai, C.J. and Nussinov, R. (2001) Molecular dynamics simulation of E-coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations. Protein Sci, 10, 135-148.
152. Ma, B., Wolfson, H.J. and Nussinov, R. (2001) Protein functional epitopes: hot spots, dynamics and combinatorial libraries. Curr Opin Struct Biol, 11, 364-369.
153. Li, W., Ma, B. and Shapiro, B.A. (2001) Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. Journal of Biomolecular Structure & Dynamics, 19, 381-396.
154. Nussinov, R., Ma, B. and Wolfson, H. (2000) Computational methods for docking and drug design:functional epitopes and combinatorial libraries. In Current topics in computational Biology. Ed. T. Jiang, T. Smith, Y. Xu and M.Q. Zhang. MIT Press, Boston, MA.
155. Ma, B., Kumar, S., Tsai, C.J., Wolfson, H., Sinha, N. and Nussinov, R. (2000) Protein-ligand interaction: induced fit? Encyclopedia in life science, London, Macmillan Reference Limited.
156. Ma, B., Lii, J.H. and Allinger, N.L. (2000) Molecular polarizabilities and induced dipole moments in molecular mechanics. Journal of Computational Chemistry, 21, 813-825.
157. Ma, B. and Nussinov, R. (2000) Molecular dynamics simulations of a b-hairpin fragment of protein G: balance between side-chain and backbone forces. J Mol Biol, 296, 1091-1104.
158. Ma, B., Kumar, S., Tsai, C.J., Hu, Z. and Nussinov, R. (2000) Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity? J Theor Biol, 203, 383-397.
159. Ma, B., Tsai, C.J. and Nussinov, R. (2000) A systematic study of the vibrational free energies of polypeptides in folded and random states. Biophys J, 79, 2739-2753.
160. Ma, B., Tsai, C.J. and Nussinov, R. (2000) Binding and folding: in search of intramolecular chaperone-like building block fragments. Protein Eng, 13, 617-627.
161. Kumar, S., Ma, B., Tsai, C.J. and Nussinov, R. (2000) Contribution of Salt Bridges Toward Protein Thermostability. J. Biomol. Struc. and Dynamics, conversation 11, 79-85.
162. Kumar, S., Ma, B., Tsai, C.J. and Nussinov, R. (2000) Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins, 38, 368-383.
163. Kumar, S., Ma, B., Tsai, C.J., Sinha, N. and Nussinov, R. (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci, 9, 10-19.
164. Hu, Z., Ma, B., Wolfson, H. and Nussinov, R. (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins, 39, 331-342.
165. Buyong, Xiong, J., Lubkowski, J. and Nussinov, R. (2000) Homology modeling and molecular dynamics simulations of lymphotactin. Protein Sci, 9, 2192-2199.
166. Tsai, C.J., Kumar, S., Ma, B. and Nussinov, R. (1999) Folding funnels, binding funnels, and protein function. Protein Sci, 8, 1181-1190.
167. Tsai, C.J., Ma, B. and Nussinov, R. (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci U S A, 96, 9970-9972.
168. Ma, B. and Nussinov, R. (1999) Explicit and implicit water simulations of a b-hairpin peptide. Proteins, 37, 73-87.
169. Ma, B., Kumar, S., Tsai, C.J. and Nussinov, R. (1999) Folding funnels and binding mechanisms. Protein Eng, 12, 713-720.
170. Lii, J.H., Ma, B. and Allinger, N.L. (1999) Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Computational Chemistry, 20, 1593-1603.
171. Kumar, S., Ma, B., Tsai, C.J., Wolfson, H. and Nussinov, R. (1999) Folding funnels and conformational transitions via hinge-bending motions. Cell Biochem Biophys, 31, 141-164.
172. Ma, B., Schaefer, H.F. and Allinger, N.L. (1998) Theoretical studies of the potential energy surfaces and compositions of the D-aldo- and D-ketohexoses. Journal of the American Chemical Society, 120, 3411-3422.
173. Kirschner, K., Ma, B., Bowen, J. and Duncan, M. (1998) Theoretical investigation of the Ca+N-2 and Ca2+N-2 complexes. CHEMICAL PHYSICS LETTERS, 295, 204-210.
174. King, R.A., Allen, W.D., Ma, B. and Schaefer, H.F. (1998) Fragmentation surface of triplet ketene. Faraday Discussions, 23-50.
175. Ma, B., Schaefer, H.F. and Allinger, N.L. (1997) Computational Studies of Structures and Reactions of Phosphate derivatives. in Recent Research Development in Chemical Science, Transworld Research Network, 1.37.
176. Ma, B., Lii, J.H., Chen, K.S. and Allinger, N.L. (1997) A molecular mechanics study of the cholesteryl acetate crystal: Evaluation of interconversion among rg, rz, and ra bond lengths. Journal of the American Chemical Society, 119, 2570-2573.
177. Ma, B. and Allinger, N.L. (1997) Calculation of rz structures from rs structures. Journal of Molecular Structure, 413, 395-404.
178. Ma, B., Collins, C.L. and Schaefer, H.F. (1996) Periodic trends for transition metal dihydrides MH2, dihydride dihydrogen complexes MH2* H-2, and tetrahydrides MH4 (M=Ti,V, and Cr). Journal of the American Chemical Society, 118, 870-879.
179. Ma, B., Lii, J.H., Schaefer, H.F. and Allinger, N.L. (1996) Systematic comparison of experimental, quantum mechanical, and molecular mechanical bond lengths for organic molecules. Journal of Physical Chemistry, 100, 8763-8769.
180. Ma, B. and Schaefer, H.F. (1996) Singlet-triplet energy separation and barrier for ring closure for trimethylenemethane and its complexes. Chemical Physics, 207, 31-41.
181. Ma, B., Lii, J.H., Chen, K.S. and Allinger, N.L. (1996) Quantum mechanical and molecular mechanics (MM3) studies of hydrazines. Journal of Physical Chemistry, 100, 11297-11304.
182. Ma, B., Allinger, N.L. and Schaefer, H.F. (1996) Spectroscopic constants and potential energy surfaces for silanone (H2SiO), hydroxysilylene (HSiOH), the hydroxysilylene dimer, and the disilynyl radical (Si2H). Journal of Chemical Physics, 105, 5731-5736.
183. Goldstein, E., Ma, B., Lii, J.H. and Allinger, N.L. (1996) Molecular mechanics calculations (MM3) on nitriles and alkynes. Journal of Physical Organic Chemistry, 9, 191-202.
184. Ma, B., Yamaguchi, Y. and Schaefer, H.F. (1995) Spectroscopic constants and potential energy surfaces for the possible interstellar molecules AlNC and AlCN. Molecular Physics, 86, 1331-1337.
185. Ma, B., Meredith, C. and Schaefer, H.F. (1995) The Quest for a Metaphosphate Intermediate - the Mechanisms for Hydrolysis of Pyrophosphates with and without Catalysis. Journal of Physical Chemistry, 99, 3815-3822.
186. Ma, B., Sulzbach, H.M., Remington, R.B. and Schaefer, H.F. (1995) Structure, Strain-Energy, and Magnetic-Susceptibility of 4-Paracyclophane and the Activation-Energy for Its Interconversion with 1,4-Tetramethylene Dewar Benzene. Journal of the American Chemical Society, 117, 8392-8400.
187. Hu, C.H., Ma, B. and Schaefer, H.F. (1995) The Synchronous Thermal-Decomposition Mechanism of Azoisopropane. Molecular Physics, 85, 769-779.
188. Souter, P.F., Andrews, L., Downs, A.J., Greene, T.M., Ma, B. and Schaefer, H.F. (1994) Observed and Calculated Raman-Spectra of the Ga2H6 and Ga2D6 Molecules. Journal of Physical Chemistry, 98, 12824-12827.
189. Ma, B. and Schaefer, H.F. (1994) Singlet Methylcarbene - Equilibrium Geometry or Transition-State. Journal of the American Chemical Society, 116, 3539-3542.
190. Ma, B., Sulzbach, H.M., Xie, Y.M. and Schaefer, H.F. (1994) p-Electron Delocalization and Compression in Acyclic Acetylenic Precursors to Multidimensional Carbon Networks - Comparison with Experiment for the Recently Synthesized Tris(Trimethylsilyl)-Substituted Tetraethynylmethane - Structures, Thermochemistry, Infrared-Spectra, Polarizabilities, and Hyperpolarizabilities. Journal of the American Chemical Society, 116, 3529-3538.
191. Ma, B. and Schaefer, H.F. (1994) Toward the Observation of Silanone (H2SiO) and Hydroxysilylene (HSiOH) Via Microwave Spectroscopy. Journal of Chemical Physics, 101, 2734-2739.
192. Ma, B., Meredith, C. and Schaefer, H.F. (1994) Pyrophosphate Structures and Reactions - Evaluation of Electrostatic Effects on the Pyrophosphates with and without Alkali Cations. Journal of Physical Chemistry, 98, 8216-8223.
193. Ma, B., Xie, Y.M., Shen, M.Z. and Schaefer, H.F. (1993) PO3-.(H2O)N Clusters - Molecular Anion Structures, Energetics, and Vibrational Frequencies. Journal of the American Chemical Society, 115, 1943-1951.
194. Ma, B., Xie, Y.M., Shen, M.Z., Schleyer, P.V. and Schaefer, H.F. (1993) Isomerization of PO3-*(H2O)N Clusters to H2PO4-*(H2O)N-1 - Transition-States and Barrier Heights. Journal of the American Chemical Society, 115, 11169-11179.
195. Ma, B., Xie, Y.M. and Schaefer, H.F. (1992) Tetraethynylethylene, a Molecule with 4 Very Short C-C Single Bonds - Interpretation of the Infrared-Spectrum. Chemical Physics Letters, 191, 521-526.