Buyong Ma

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states
    Yifat Miller
    Center for Cancer Research Nanobiology Program NCI Frederick, Frederick, MD 21702, USA
    Biochemistry 50:5172-81. 2011
  2. pmc Cooperativity among short amyloid stretches in long amyloidogenic sequences
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 7:e39369. 2012
  3. pmc Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP
    Yu Xu
    Institute of Chinese Minority Traditional Medicine, Minzu University of China, Beijing 100081, People s Republic of China
    J Phys Chem B 116:4801-11. 2012
  4. ncbi request reprint Druggable orthosteric and allosteric hot spots to target protein-protein interactions
    Buyong Ma
    Basic Science Program, Leidos Biomedical Research, Inc Cancer and Inflammation Program, NCIFrederick, Frederick, MD 21702
    Curr Pharm Des 20:1293-301. 2014
  5. doi request reprint Structured crowding and its effects on enzyme catalysis
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
    Top Curr Chem 337:123-37. 2013
  6. pmc Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide
    Buyong Ma
    SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI, National Institutes of Health, Frederick, Maryland 21702, USA
    J Biol Chem 286:34244-53. 2011
  7. pmc Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, USA
    J Biol Chem 285:37102-10. 2010
  8. doi request reprint Enzyme dynamics point to stepwise conformational selection in catalysis
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Curr Opin Chem Biol 14:652-9. 2010
  9. ncbi request reprint CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible
    Yongping Pan
    Basic Research Program, SAIC Frederick, Inc Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, MD 21702, USA
    J Mol Biol 350:514-27. 2005
  10. ncbi request reprint The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, MD 21702, USA
    Phys Biol 2:S56-66. 2005

Detail Information

Publications62

  1. pmc Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states
    Yifat Miller
    Center for Cancer Research Nanobiology Program NCI Frederick, Frederick, MD 21702, USA
    Biochemistry 50:5172-81. 2011
    ..We suggest that the polymorphic tau and Aβ-tau aggregates may be largely due to repeat sequences which are prone to variable turn locations along the tau repeats...
  2. pmc Cooperativity among short amyloid stretches in long amyloidogenic sequences
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 7:e39369. 2012
    ..Our study revealed that genome-wide amyloid segments are not only dependent on short high propensity stretches, but also on nearby residues...
  3. pmc Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP
    Yu Xu
    Institute of Chinese Minority Traditional Medicine, Minzu University of China, Beijing 100081, People s Republic of China
    J Phys Chem B 116:4801-11. 2012
    ..Our study indicates that evolution has optimized the inter-relationship between proteins and DNA/RNA, which requires overall changes at the molecular and systems biology levels when replacing phosphate by arsenate. ..
  4. ncbi request reprint Druggable orthosteric and allosteric hot spots to target protein-protein interactions
    Buyong Ma
    Basic Science Program, Leidos Biomedical Research, Inc Cancer and Inflammation Program, NCIFrederick, Frederick, MD 21702
    Curr Pharm Des 20:1293-301. 2014
    ..While detection of allosteric hot spots is challenging, targeting drugs to these residues has the potential of greatly increasing the hot spot and protein druggability. ..
  5. doi request reprint Structured crowding and its effects on enzyme catalysis
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
    Top Curr Chem 337:123-37. 2013
    ..More likely, they too transmit allosteric effects, and as such play important functional roles. Overall, structured cellular crowding may lead to higher enzyme efficiency and specificity. ..
  6. pmc Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide
    Buyong Ma
    SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI, National Institutes of Health, Frederick, Maryland 21702, USA
    J Biol Chem 286:34244-53. 2011
    ....
  7. pmc Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, USA
    J Biol Chem 285:37102-10. 2010
    ..Our results call attention to the possible existence of certain "critical intermediates" that can lead to both seeds and other soluble ADDL-like oligomers...
  8. doi request reprint Enzyme dynamics point to stepwise conformational selection in catalysis
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Curr Opin Chem Biol 14:652-9. 2010
    ..Within such a framework, entropy can have a larger role in conformational dynamics than in direct energy transfer in dynamically promoted catalysis...
  9. ncbi request reprint CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible
    Yongping Pan
    Basic Research Program, SAIC Frederick, Inc Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, MD 21702, USA
    J Mol Biol 350:514-27. 2005
    ....
  10. ncbi request reprint The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, MD 21702, USA
    Phys Biol 2:S56-66. 2005
    ..Met384/Phe385 in the C-terminal region interacts with the S100B protein and the Bromodomain of the CBP protein. Thus, these residues may assist in elucidating the p53 interactions when structural data are not available...
  11. ncbi request reprint Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19
    David Zanuy
    Laboratory of Experimental and Computational Biology, NCI Frederick, Bldg 469, Rm 151, Frederick, MD 21702, USA
    Phys Biol 1:89-99. 2004
    ..In terms of structural biology, our results clearly indicate that an amyloid organization implies a degree of complexity far beyond a simple nonspecific association of peptide strands via amide hydrogen bonds...
  12. ncbi request reprint Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain
    Yongping Pan
    Basic Research Program, Science Applications International Corporation Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
    J Biol Chem 279:30523-30. 2004
    ....
  13. ncbi request reprint Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, National Institutes of Health, Frederick, MD 21702, USA
    J Biol Chem 279:53875-85. 2004
    ..The unified conformational control and the shapes of eRF1 and RF2 support the proposition that the termination of protein synthesis involves similar mechanisms across species...
  14. pmc Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35
    Jie Zheng
    Basic Research Program, SAIC Frederick, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, Maryland 21702, USA
    Biophys J 91:824-33. 2006
    ..Mutant simulations show that substitution of Asn-2, Gln-4, or Asn-6 by Ala would disrupt this steric zipper, leading to unstable oligomers...
  15. pmc Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities
    Jie Zheng
    Basic Research Program, SAIC Frederick Center for Cancer Research, Nanobiology Program, NCI Frederick, Frederick, Maryland 21702, USA
    Biophys J 93:3046-57. 2007
    ..Thus, we propose that Abeta fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging...
  16. ncbi request reprint Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure
    Jie Zheng
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Phys Biol 3:P1-4. 2006
    ....
  17. ncbi request reprint Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Curr Top Med Chem 7:999-1005. 2007
    ..Thus, this may suggest that nature tends to avoid Ile conservation in protein-protein interaction to avoid amyloid formation. In this regards, Trp/Met/Phe as well as Ile may be targeted to modulate protein-protein interaction...
  18. ncbi request reprint Insights into amyloid structural formation and assembly through computational approaches
    David Zanuy
    Laboratory of Experimental and Computational Biology, NCI Frederick, Bldg 469, Rm 151, Frederick, MD 21702, USA
    Amyloid 11:143-61. 2004
    ..Ultimately, obtaining molecular structures should facilitate efforts to therapy and drug design...
  19. pmc Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 102:3988-93. 2005
    ..Thus, they have significant implications toward our understanding of DNA binding by p53 as well as p53-mediated interactions with other proteins...
  20. pmc "Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains
    Jin Liu
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, National Cancer Institute Frederick, Frederick, Maryland 21702, USA
    Structure 14:1811-21. 2006
    ..Hence, falling into the "similarity trap" may disrupt normal BRCA1 and p53 functions. Our results illustrate how this trap is avoided in the native state...
  21. pmc Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation
    Yifat Miller
    Center for Cancer Research Nanobiology Program, National Cancer Institute Frederick, Frederick, Maryland, USA
    Biophys J 97:1168-77. 2009
    ....
  22. doi request reprint Dynamic allostery: linkers are not merely flexible
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Structure 19:907-17. 2011
    ..We further propose that evolution has optimized the linker sequences and lengths for efficiency, which explains why mutations in linkers may affect protein function and review the literature in this light...
  23. pmc Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
    Protein Sci 12:1882-93. 2003
    ..The limited variation of topological space, compared with the number of possible sequence changes, may relate to the observation that the number of known protein folds are far less than the sequential allowance...
  24. pmc The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant
    Buyong Ma
    Basic Research Program, SAIC Frederick, Center for Cancer Research, Nanobiology Program, National Cancer Institute, FCRDC, Frederick, Maryland 21702, USA
    Biophys J 90:3365-74. 2006
    ..One conceivable approach is to stabilize the intermediates to deter amyloid formation...
  25. pmc Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels
    Hyunbum Jang
    Center for Cancer Research Nanobiology Program, NCI Frederick, SAIC Frederick, Frederick, Maryland, USA
    Biophys J 95:4631-42. 2008
    ..Consistent with the toxic beta-amyloid channels that are ion-conducting, the PG-1 channels permeate anions...
  26. pmc Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect
    Hyunbum Jang
    Center for Cancer Research Nanobiology Program, SAIC Frederick, Inc, NCI Frederick, Frederick, Maryland 21702, USA
    BMC Struct Biol 7:21. 2007
    ..The experimental structure of the PG-1 dimer is currently unavailable...
  27. ncbi request reprint In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1
    Yongping Pan
    Basic Research Program, SAIC Frederick, Incorporated, Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, Maryland 21702, USA
    Biochemistry 44:1423-32. 2005
    ..Linearity (i.e., nonbranched), moderate size, and balanced hydrophobic and hydrophilic properties of the side chain are crucial to the stabilizing effect of the residue substitutions...
  28. pmc The stability and dynamics of the human calcitonin amyloid peptide DFNKF
    Hui Hsu Tsai
    Basic Research Program, Science Applications International Corporation Frederick, Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
    Biophys J 87:146-58. 2004
    ..Simulations of mutants and capped peptides show that both interstrand hydrophobic and electrostatic interactions play important roles in stabilizing the DFNKF parallel oligomers. This study provides insights into amyloid formation...
  29. pmc Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?
    Buyong Ma
    SAIC Frederick, Inc, NCI Frederick, Maryland 21702, USA
    ACS Chem Biol 5:265-72. 2010
    ..Allosteric effects can enhance the binding specificity in a function-oriented manner. Here we provide a biological rationale that considers cellular crowding effects...
  30. doi request reprint Mechanisms of transcription factor selectivity
    Yongping Pan
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Trends Genet 26:75-83. 2010
    ..The classification of TF recognition mechanisms based on these factors impacts our understanding of how transcription initiation is regulated...
  31. pmc Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH
    Yifat Miller
    Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 107:14128-33. 2010
    ..The existence of the hollow core fibril at physiological pH emphasizes the need to examine toxic effects of minor oligomeric species with unique organizations...
  32. pmc Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 35:7733-47. 2007
    ..Our work suggests that p53 needs balanced binding modes to maintain genome stability. Inverse repeat p53REs favor the H14 mode and direct repeat p53REs may have high possibilities of other modes...
  33. doi request reprint Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control
    Chung Jung Tsai
    Basic Research Program, SAIC Frederick Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Phys Biol 6:013001. 2009
    ..If the N-terminal is subsequently cleaved, the protein can be under kinetic control, since it is trapped in a thermodynamically less-stable state...
  34. pmc Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets
    Buyong Ma
    Basic Research Program, SAIC Frederick Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Nucleic Acids Res 35:2986-3001. 2007
    ..We propose that the palindromic sequence couplings may encode such potential preferred multiple binding modes of the p53 tetramer to DNA...
  35. pmc Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL
    David Zanuy
    Laboratory of Experimental and Computational Biology, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, Maryland 21702, USA
    Biophys J 84:1884-94. 2003
    ....
  36. doi request reprint Allosteric conformational barcodes direct signaling in the cell
    Ruth Nussinov
    Basic Science Program, SAIC Frederick, Inc, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel Electronic address
    Structure 21:1509-21. 2013
    ....
  37. pmc Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations
    Wen Li
    Laboratory of Experimental and Computational Biology, The NCI Center for Cancer Research, National Cancer Institute Frederick, National Institutes of Health, Building 469, Room 150, Frederick, MD 21702, USA
    Nucleic Acids Res 31:629-38. 2003
    ..The negatively charged phosphate groups of G658, U740, G741 and G742 bind to the positively charged S15 residues Lys7, Arg34 and Arg37. The current study provides a dynamic view of the binding of 16S rRNA with S15...
  38. pmc Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 100:5772-7. 2003
    ..A hybrid strategy, mapping sequence alignment onto a single structure illustrates the possibility of binding site identification around these three residues...
  39. ncbi request reprint Triggering loops and enzyme function: identification of loops that trigger and modulate movements
    K Gunasekaran
    Basic Research Program, SAIC Frederick Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, Bldg 469 Rm 151, Frederick, MD 21702, USA
    J Mol Biol 332:143-59. 2003
    ..Mechanisms may be conserved across different folds, sequences and functions, with adaptation to specific enzymatic roles...
  40. pmc Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome
    Yu Xu
    Institute of Chinese Minority Traditional Medicine, Minzu University of China, Beijing, P R China
    Proteomics 13:1339-51. 2013
    ..It is interesting to note that the minimal genome model based on the charge and mass of Escherichia coli may have a larger protein-protein interaction network than that based on the lower organism Mycoplasma pneumoniae...
  41. ncbi request reprint Is allostery an intrinsic property of all dynamic proteins?
    K Gunasekaran
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, National Cancer Institute Frederick, Bldg 469, Rm 151, Frederick, Maryland 21702, USA
    Proteins 57:433-43. 2004
    ..The question is its effectiveness in the redistribution of the ensemble, affecting the protein binding sites and its function. Here, we review experimental observations validating this view of protein allostery...
  42. ncbi request reprint Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    Buyong Ma
    Basic Research Program, SAIC Frederick Inc, Center for Cancer Research, Nanobiology Program, NCI Frederick, Frederick MD 21702, USA
    Curr Opin Chem Biol 10:445-52. 2006
    ..Under kinetic control, the final protein aggregations are the outcome of maximizing the van der Waals interactions between side chains and backbone hydrogen bonds...
  43. doi request reprint A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery
    Ruth Nussinov
    Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
    Biochim Biophys Acta 1834:820-9. 2013
    ..This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly...
  44. pmc In silico protein design by combinatorial assembly of protein building blocks
    Hui Hsu Gavin Tsai
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, Building 469, Room 145, Frederick, MD 21702, USA
    Protein Sci 13:2753-65. 2004
    ..Such an approach provides a new method for engineering new proteins with similar folds and low homology...
  45. pmc Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation
    Buyong Ma
    Laboratory of Experimental and Computational Biology, National Cancer Institute at Frederick, Maryland 21702, USA
    Protein Sci 11:2335-50. 2002
    ..Our simulations of the prion-derived 8-residue amyloidogenic peptide and its variant have indicated that an octamer is stable enough to be a seed and that the driving force for stabilization is the hydrophobic effect...
  46. pmc Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects
    Buyong Ma
    Laboratory of Experimental and Computational Biology, and Intramural Research Support Program, Science Applications International Corporation, National Cancer Institute, Building 469, Room 151, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 99:14126-31. 2002
    ..An intra-strand salt-bridge (D23-K28) stabilizes the bent hairpin-like hook structure. The bent double-beta-sheet model for the Abeta(10-35) similarly offers oligomer stability...
  47. pmc Interaction of protegrin-1 with lipid bilayers: membrane thinning effect
    Hyunbum Jang
    Center for Cancer Research Nanobiology Program, SAIC Frederick, Inc, NCI Frederick, Frederick, Maryland 21702, USA
    Biophys J 91:2848-59. 2006
    ..The thinning effects in the bilayer should relate to pore/channel formation in the lipid bilayer and thus be responsible for further defects in the membrane caused by oligomer...
  48. pmc Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states
    Yifat Miller
    Center for Cancer Research Nanobiology Program, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 107:9490-5. 2010
    ....
  49. ncbi request reprint Comparison of the human and worm p53 structures suggests a way for enhancing stability
    Yongping Pan
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, Maryland 21702, USA
    Biochemistry 45:3925-33. 2006
    ..In addition, loop- or turn-related mutants with different stabilities may also be used to probe the relationship between function, a particular structural motif, and its flexibility...
  50. doi request reprint The underappreciated role of allostery in the cellular network
    Ruth Nussinov
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, Maryland 21702, USA
    Annu Rev Biophys 42:169-89. 2013
    ..The challenges are colossal; the inspiring reward will be predicting function, misfunction, and outcomes of drug regimes...
  51. ncbi request reprint Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI FCRDC, Frederick, MD 21702, USA
    Protein Eng 16:561-75. 2003
    ..These conformational changes may relate to polymerization tendencies of these variants...
  52. doi request reprint Protein-protein interaction networks: how can a hub protein bind so many different partners?
    Chung Jung Tsai
    Center for Cancer Research Nanobiology Program, SAIC Frederick, Inc, NCI Frederick, Frederick, MD 21702, USA
    Trends Biochem Sci 34:594-600. 2009
    ..This leads to the impression that a single protein binds to a very large number of partners. In reality, it does not; rather, protein networks reflect the combination of multiple proteins, each with a distinct conformation...
  53. ncbi request reprint Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I
    K Gunasekaran
    Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, Maryland 21702, USA
    Biochemistry 42:3674-87. 2003
    ..These observations lead us to propose a new functional mechanism that may be conserved by evolution to perform a variety of functions...
  54. doi request reprint Selective molecular recognition in amyloid growth and transmission and cross-species barriers
    Buyong Ma
    Basic Science Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    J Mol Biol 421:172-84. 2012
    ..In particular, we argue that recent theoretical and experimental observations support the key role of selective molecular recognition in amyloidosis and in determining cross-species barriers and transmission...
  55. pmc Regulating highly dynamic unstructured proteins and their coding mRNAs
    Buyong Ma
    Basic Research Program, SAIC Frederick Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    Genome Biol 10:204. 2009
    ..The lifetimes and conformations of intrinsically unstructured proteins (IUPs) and their mRNAs are orchestrated to ensure precision, speed and flexibility in biological control...
  56. doi request reprint Multiple conformational selection and induced fit events take place in allosteric propagation
    Ruth Nussinov
    Leidos Biomedical Research, Inc, Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States Sackler Inst of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel Electronic address
    Biophys Chem 186:22-30. 2014
    ..Thus, as in binding, the allosteric effects induced by PTMs and light relate not only to population shift; but to conformational selection as well. Conformational selection and population shift take place conjointly. ..
  57. ncbi request reprint From computational quantum chemistry to computational biology: experiments and computations are (full) partners
    Buyong Ma
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, MD 21702, USA
    Phys Biol 1:P23-6. 2004
    ..For the perception to become reality, computation and experiment should be united as full partners in biological research...
  58. ncbi request reprint Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway
    Yuk Yin Sham
    Laboratory of Experimental and Computational Biology, NCI Frederick, Frederick, Maryland, USA
    Proteins 46:308-20. 2002
    ..coli dihydrofolate reductase involves sequential formation of the substrate binding sites...
  59. pmc The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions
    Yifat Miller
    Center for Cancer Research Nanobiology Program NCI Frederick, Frederick, Maryland 21702, USA
    J Am Chem Soc 133:2742-8. 2011
    ..Our findings, together with the recent cyroEM characterization of the hollow core in Aβ(1-42) fibrils, point to the relevance of a cavity in Aβ(1-40/1-42) oligomers which should be considered when targeting oligomer toxicity...
  60. pmc Crystal structure of a plectonemic RNA supercoil
    Jason R Stagno
    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
    Nat Commun 3:901. 2012
    ..Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids...
  61. pmc Protein dynamics and conformational selection in bidirectional signal transduction
    Ruth Nussinov
    Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
    BMC Biol 10:2. 2012
    ....
  62. pmc Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations
    Buyong Ma
    Laboratory of Experimental and Computational Biology, National Cancer Institute Frederick, Frederick, Maryland 21702, USA
    Protein Sci 11:184-97. 2002
    ..It provides a rationale for higher affinity inhibitors that are not derived from substrates at their transition states and indicates flexible docking schemes...