Research Topics
| Buyong MaSummaryAffiliation: National Institutes of Health Country: USA Publications
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Detail Information
Publications
Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptideBuyong 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....
Enzyme dynamics point to stepwise conformational selection in catalysisBuyong 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...- Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamerBuyong 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... 
CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexibleYongping 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....- The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteinsBuyong 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... - Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domainYongping 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.... - Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19David 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... - Release factors eRF1 and RF2: a universal mechanism controls the large conformational changesBuyong 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... - Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavitiesJie 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... - Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35Jie 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... - Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug designBuyong 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... - Insights into amyloid structural formation and assembly through computational approachesDavid 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... - Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interfaceBuyong 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... - Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structureJie 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.... - "Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domainsJin 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... - The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutantBuyong 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... - Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequencesBuyong 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... - Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channelsHyunbum 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... - Dynamic allostery: linkers are not merely flexibleBuyong 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... - 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... - Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effectHyunbum 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... - Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformationYifat Miller
Center for Cancer Research Nanobiology Program, National Cancer Institute Frederick, Frederick, Maryland, USA
Biophys J 97:1168-77. 2009.... - Mechanisms of transcription factor selectivityYongping 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... - The stability and dynamics of the human calcitonin amyloid peptide DFNKFHui-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... - In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1Yongping 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... - Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pHYifat 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... - Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targetsBuyong 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... - Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAILDavid 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.... - Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic controlChung 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... - Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elementsBuyong 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... - Triggering loops and enzyme function: identification of loops that trigger and modulate movementsK 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... - Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfacesBuyong 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... - Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulationsWen 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... - Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formationBuyong 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... - Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effectsBuyong 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... - Interaction of protegrin-1 with lipid bilayers: membrane thinning effectHyunbum 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... - Comparison of the human and worm p53 structures suggests a way for enhancing stabilityYongping 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... - In silico protein design by combinatorial assembly of protein building blocksHui-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... - Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic statesYifat 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.... - 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... - Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-IK 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... - 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... - Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variantsBuyong 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... - Selective molecular recognition in amyloid growth and transmission and cross-species barriersBuyong 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... - Regulating highly dynamic unstructured proteins and their coding mRNAsBuyong 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... - Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathwayYuk 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... - Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic statesYifat 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... - The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditionsYifat 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... - From computational quantum chemistry to computational biology: experiments and computations are (full) partnersBuyong 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... - Crystal structure of a plectonemic RNA supercoilJason 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... - Protein dynamics and conformational selection in bidirectional signal transductionRuth Nussinov
Basic Research Program, SAIC Frederick, Inc, Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
BMC Biol 10:2. 2012.... - Multiple diverse ligands binding at a single protein site: a matter of pre-existing populationsBuyong 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...