Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants
暂无分享,去创建一个
Maxwell D. Sanderford | Sudhir Kumar | S. Ozkan | I. C. Kazan | Brandon M. Butler | Avishek Kumar | Nicholas J. Ose
[1] S. Banu Ozkan,et al. Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity , 2021, Nature Communications.
[2] S. Ozkan,et al. Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions , 2020, Molecular biology and evolution.
[3] S. Banu Ozkan,et al. Allostery and Epistasis: Emergent Properties of Anisotropic Networks , 2020, Entropy.
[4] Luca Ponzoni,et al. Rhapsody: predicting the pathogenicity of human missense variants , 2020, Bioinform..
[5] Sudhir Kumar,et al. The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution. , 2020, Annual review of biophysics.
[6] F. Arnold,et al. Engineering new catalytic activities in enzymes , 2020, Nature Catalysis.
[7] N. Ben-Tal,et al. ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins , 2019, Protein science : a publication of the Protein Society.
[8] E. Sidransky,et al. Glucocerebrosidase and its relevance to Parkinson disease , 2019, Molecular Neurodegeneration.
[9] Ashley M Buckle,et al. Protein engineering: the potential of remote mutations. , 2019, Biochemical Society transactions.
[10] Arvind Ramanathan,et al. Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning , 2019, Proceedings of the National Academy of Sciences.
[11] S. Ozkan,et al. Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-lactamase , 2018, International journal of molecular sciences.
[12] Brandon M Butler,et al. Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs , 2018, PLoS Comput. Biol..
[13] Sudhir Kumar,et al. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.
[14] V. Hilser,et al. Dynamic allostery can drive cold adaptation in enzymes , 2018, Nature.
[15] Ivet Bahar,et al. Structural dynamics is a determinant of the functional significance of missense variants , 2018, Proceedings of the National Academy of Sciences.
[16] K. Ghosh,et al. Ancient Thioredoxins Evolved to Modern Day Stability-Function Requirement by Altering Native State Ensemble , 2018, bioRxiv.
[17] Benjamin T. Porebski,et al. The role of protein dynamics in the evolution of new enzyme function. , 2016, Nature chemical biology.
[18] L. Swint-Kruse. Using Evolution to Guide Protein Engineering: The Devil IS in the Details. , 2016, Biophysical journal.
[19] Geir Villy Isaksen,et al. Enzyme surface rigidity tunes the temperature dependence of catalytic rates , 2016, Proceedings of the National Academy of Sciences.
[20] Ruth Nussinov,et al. Allostery: An Overview of Its History, Concepts, Methods, and Applications , 2016, PLoS Comput. Biol..
[21] Ben M. Webb,et al. Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.
[22] Lucas Sawle,et al. Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma. , 2016, Journal of chemical theory and computation.
[23] Sudhir Kumar,et al. Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine. , 2015, Current opinion in structural biology.
[24] C. Margulis,et al. A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs. , 2015, Biochemistry.
[25] Tyler J. Glembo,et al. The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin. , 2015, Biophysical journal.
[26] C. Simmerling,et al. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.
[27] István A. Kovács,et al. Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders , 2015, Cell.
[28] Sudhir Kumar,et al. Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association , 2015, Proteins.
[29] S. Ozkan,et al. A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. , 2015, Structure.
[30] K N Houk,et al. The Role of Distant Mutations and Allosteric Regulation on LovD Active Site Dynamics , 2014, Nature chemical biology.
[31] Frances M. G. Pearl,et al. Deriving a Mutation Index of Carcinogenicity Using Protein Structure and Protein Interfaces , 2014, PloS one.
[32] Janet M. Thornton,et al. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes , 2013, Nucleic Acids Res..
[33] Adam Godzik,et al. Divergent evolution of protein conformational dynamics in dihydrofolate reductase , 2013, Nature Structural &Molecular Biology.
[34] Duncan Poole,et al. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.
[35] R. Nussinov,et al. Allostery in Disease and in Drug Discovery , 2013, Cell.
[36] Sudhir Kumar,et al. Structural dynamics flexibility informs function and evolution at a proteome scale , 2013, Evolutionary applications.
[37] Roland L. Dunbrack,et al. Prediction of phenotypes of missense mutations in human proteins from biological assemblies , 2013, Proteins.
[38] I. Adzhubei,et al. Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.
[39] Vanessa E. Gray,et al. Evolutionary diagnosis method for variants in personal exomes , 2012, Nature Methods.
[40] Z. Nevin Gerek,et al. Collective Dynamics Differentiates Functional Divergence in Protein Evolution , 2012, PLoS Comput. Biol..
[41] Haiyuan Yu,et al. Three-dimensional reconstruction of protein networks provides insight into human genetic disease , 2012, Nature Biotechnology.
[42] R. L. Lieberman,et al. A Guided Tour of the Structural Biology of Gaucher Disease: Acid-β-Glucosidase and Saposin C , 2011, Enzyme research.
[43] J. Dudley,et al. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. , 2011, Trends in genetics : TIG.
[44] G. Robertson,et al. Therapeutic Implications of Targeting AKT Signaling in Melanoma , 2011, Enzyme research.
[45] E. Sidransky,et al. The Role of Glucocerebrosidase Mutations in Parkinson Disease and Lewy Body Disorders , 2010, Current neurology and neuroscience reports.
[46] P. Bork,et al. A method and server for predicting damaging missense mutations , 2010, Nature Methods.
[47] Ali Rana Atilgan,et al. Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein , 2009, PLoS Comput. Biol..
[48] Jie Liang,et al. Ethnic Differences and Functional Analysis of MET Mutations in Lung Cancer , 2009, Clinical Cancer Research.
[49] Sudhir Kumar,et al. Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. , 2009, Genome research.
[50] K. Marder,et al. Association of glucocerebrosidase mutations with dementia with lewy bodies. , 2009, Archives of neurology.
[51] Nir Ben-Tal,et al. The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures , 2008, Nucleic Acids Res..
[52] Pietro Liò,et al. Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms , 2008, PLoS Comput. Biol..
[53] E. Sidransky,et al. Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene (GBA) , 2008, Human mutation.
[54] K. Marder,et al. Mutations in the glucocerebrosidase gene are associated with early-onset Parkinson disease , 2007, Neurology.
[55] Hui Lu,et al. Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP) , 2007, Bioinform..
[56] Gregory A Petsko,et al. Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. , 2006, Nature chemical biology.
[57] Emidio Capriotti,et al. Bioinformatics Original Paper Predicting the Insurgence of Human Genetic Diseases Associated to Single Point Protein Mutations with Support Vector Machines and Evolutionary Information , 2022 .
[58] Min Zhang,et al. Analyses of variant acid beta-glucosidases: effects of Gaucher disease mutations. , 2006, The Journal of biological chemistry.
[59] J. Moult,et al. Loss of protein structure stability as a major causative factor in monogenic disease. , 2005, Journal of molecular biology.
[60] D. Elstein,et al. The glucocerebrosidase gene and Parkinson's disease in Ashkenazi Jews. , 2005, The New England journal of medicine.
[61] J. Aharon-Peretz,et al. Mutations in the glucocerebrosidase gene and Parkinson's disease in Ashkenazi Jews. , 2004, The New England journal of medicine.
[62] J. Sussman,et al. X‐ray structure of human acid‐β‐glucosidase, the defective enzyme in Gaucher disease , 2003, EMBO reports.
[63] P. Stenson,et al. Human Gene Mutation Database (HGMD®): 2003 update , 2003, Human mutation.
[64] L. Serrano,et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.
[65] H. Berman,et al. Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank , 2022 .
[66] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[67] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[68] Peter A. Kollman,et al. Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model , 1995, J. Comput. Chem..
[69] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[70] H. Edelsbrunner,et al. Efficient algorithms for agglomerative hierarchical clustering methods , 1984 .
[71] J. A. Gavira,et al. Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. , 2015, Molecular biology and evolution.
[72] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[73] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[74] T. Alber,et al. Mutational effects on protein stability. , 1989, Annual review of biochemistry.