Carla Mattos
Works (28)
Updated: July 7th, 2023 21:17
2020 journal article
DRoP: Automated detection of conserved solvent-binding sites on proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 88(1), 152–165.
author keywords: conserved solvent positions; DRoP software; protein hydration; protein multiple crystal structures; RNase A; water analysis program
MeSH headings : Animals; Binding Sites; Cattle; Crystallography, X-Ray; Databases, Protein; Humans; Ligands; Models, Molecular; Organic Chemicals / chemistry; Protein Binding; Protein Conformation; Proteins / chemistry; Ribonuclease, Pancreatic / chemistry; Software; Solvents / chemistry; Water / chemistry
Source: Web Of Science
Added: August 12, 2019
2020 article
Exploring the Rap1A Active Site Through Accelerated Molecular Dynamic Simulations
Schwabe, M., Holzapfel, G., & Mattos, C. (2020, April). FASEB JOURNAL, Vol. 34.
Source: Web Of Science
Added: October 12, 2020
2019 journal article
Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 75(2), 111–115.
author keywords: in crystallo titration; neutron crystallography; pK(a); protonation; radiation damage
MeSH headings : Crystallization; Humans; Hydrogen-Ion Concentration; Models, Molecular; Monomeric GTP-Binding Proteins / chemistry; Neutron Diffraction / methods; Protein Binding; Protein Conformation
Sources: Web Of Science, ORCID
Added: February 18, 2019
2018 journal article
Neutron scattering in the biological sciences: progress and prospects
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 74, 1129–1168.
author keywords: neutron scattering; biological systems; structure and dynamics
MeSH headings : Animals; Crystallography / methods; Deuterium / analysis; Deuterium Exchange Measurement / methods; Humans; Models, Molecular; Neutron Diffraction / methods; Neutrons; Proteins / chemistry
Sources: Web Of Science, ORCID
Added: January 21, 2019
2015 journal article
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD
STRUCTURE, 23(3), 505–516.
MeSH headings : Allosteric Regulation; Catalytic Domain; Crystallography, X-Ray; Humans; Hydrogen Bonding; Molecular Dynamics Simulation; Mutation, Missense; Protein Binding; Protein Interaction Domains and Motifs; Protein Structure, Quaternary; Protein Structure, Secondary; Proto-Oncogene Proteins c-raf / chemistry; Proto-Oncogene Proteins p21(ras) / chemistry; Proto-Oncogene Proteins p21(ras) / genetics
doi.org (publisher)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP gamma-Phosphate
JOURNAL OF BIOLOGICAL CHEMISTRY, 290(52), 31025–31036.
MeSH headings : Catalysis; Guanosine Triphosphate / analogs & derivatives; Guanosine Triphosphate / chemistry; Guanosine Triphosphate / genetics; Guanosine Triphosphate / metabolism; Humans; Hydrolysis; Neutrons; Protein Structure, Tertiary; Proto-Oncogene Proteins p21(ras) / chemistry; Proto-Oncogene Proteins p21(ras) / genetics; Proto-Oncogene Proteins p21(ras) / metabolism
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 journal article
DRoP: A Water Analysis Program Identifies Ras-GTP-Specific Pathway of Communication between Membrane-Interacting Regions and the Active Site
JOURNAL OF MOLECULAR BIOLOGY, 426(3), 611–629.
author keywords: crystallographic water analysis; Ras GTPase; water-mediated networks in protein structure; protein hydration; DRoP software
MeSH headings : Catalytic Domain; Cell Membrane / metabolism; Crystallography; Crystallography, X-Ray; Guanosine Triphosphate / metabolism; Models, Molecular; Mutagenesis, Site-Directed; Mutation / genetics; Protein Binding; Protein Conformation; Signal Transduction; Water / metabolism; ras Proteins / chemistry; ras Proteins / genetics; ras Proteins / metabolism
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Allosteric modulation of caspase 3 through mutagenesis
BIOSCIENCE REPORTS, 32(4), 401–411.
author keywords: allosteric site; apoptosis; caspase; inhibition; protein ensemble
MeSH headings : Allosteric Regulation / genetics; Allosteric Site / genetics; Amino Acid Substitution; Caspase 3 / chemistry; Caspase 3 / genetics; Catalytic Domain; Crystallography, X-Ray; Humans; Hydrogen Bonding; Molecular Dynamics Simulation; Mutagenesis, Site-Directed; Protein Interaction Domains and Motifs; Protein Structure, Secondary
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition
BIOCHEMISTRY, 51(31), 6114–6126.
MeSH headings : Acetates / metabolism; Acetates / pharmacology; Allosteric Regulation / drug effects; Allosteric Site / drug effects; Calcium Compounds / metabolism; Calcium Compounds / pharmacology; Catalytic Domain; Dithioerythritol / metabolism; Dithioerythritol / pharmacology; Dithiothreitol / metabolism; Dithiothreitol / pharmacology; Enzyme Stability / drug effects; Guanosine Triphosphate / metabolism; Guanylyl Imidodiphosphate / chemistry; Hydrolysis; Isoenzymes / chemistry; Isoenzymes / metabolism; Models, Molecular; Polyethylene Glycols / pharmacology; Protein Structure, Secondary; Small Molecule Libraries / metabolism; Small Molecule Libraries / pharmacology; Solutions; Solvents / chemistry; Solvents / pharmacology; ras Proteins / chemistry; ras Proteins / metabolism
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity
JOURNAL OF BIOLOGICAL CHEMISTRY, 287(23), 19418–19428.
MeSH headings : Archaeal Proteins / chemistry; Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Chromosomal Proteins, Non-Histone / chemistry; Chromosomal Proteins, Non-Histone / genetics; Chromosomal Proteins, Non-Histone / metabolism; Methanococcales / chemistry; Methanococcales / genetics; Methanococcales / metabolism; Methyltransferases / chemistry; Methyltransferases / genetics; Methyltransferases / metabolism; Protein Binding; Protein Structure, Tertiary; Ribonucleoproteins / chemistry; Ribonucleoproteins / genetics; Ribonucleoproteins / metabolism
Source: Web Of Science
Added: August 6, 2018
2011 journal article
Allosteric Modulation of Ras-GTP Is Linked to Signal Transduction through RAF Kinase
JOURNAL OF BIOLOGICAL CHEMISTRY, 286(5), 3323–3331.
MeSH headings : Allosteric Regulation; Allosteric Site; Animals; Guanosine Triphosphate / metabolism; Kinetics; Mice; Mutation, Missense; NIH 3T3 Cells; Protein Conformation; Protein Stability; Signal Transduction; raf Kinases / metabolism; ras Proteins / genetics; ras Proteins / metabolism
Sources: Web Of Science, ORCID
Added: August 6, 2018
2011 journal article
Comparative Analysis of the 15.5kD Box C/D snoRNP Core Protein in the Primitive Eukaryote Giardia lamblia Reveals Unique Structural and Functional Features
BIOCHEMISTRY, 50(14), 2907–2918.
MeSH headings : Amino Acid Sequence; Animals; Binding Sites / genetics; Circular Dichroism; Crystallography, X-Ray; Giardia lamblia / metabolism; Humans; Methyltransferases / chemistry; Methyltransferases / metabolism; Models, Molecular; Molecular Sequence Data; Molecular Weight; Phylogeny; Protein Binding; Protein Stability; Protein Structure, Secondary; Protein Structure, Tertiary; Protozoan Proteins / chemistry; Protozoan Proteins / genetics; Protozoan Proteins / metabolism; RNA / genetics; RNA / metabolism; Ribonucleoproteins, Small Nucleolar / chemistry; Ribonucleoproteins, Small Nucleolar / classification; Ribonucleoproteins, Small Nucleolar / metabolism; Sequence Homology, Amino Acid; Temperature
Source: Web Of Science
Added: August 6, 2018
2011 journal article
Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 508(1), 31–38.
author keywords: Apoptosis; Caspase activation; Enzyme activity; Protein folding and assembly
MeSH headings : Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Catalytic Domain; Crystallography, X-Ray; Enzyme Stability; Hydrogen Bonding; Models, Molecular; Mutation; Protein Folding; Static Electricity; Structure-Activity Relationship; Thermodynamics
Source: Web Of Science
Added: August 6, 2018
2010 journal article
Allosteric modulation of Ras positions Q61 for a direct role in catalysis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107(11), 4931–4936.
author keywords: GTPase; Raf; calcium; intrinsic hydrolysis
MeSH headings : Acetates / pharmacology; Allosteric Regulation / drug effects; Allosteric Site; Biocatalysis / drug effects; Calcium / metabolism; Calcium Compounds / pharmacology; Catalytic Domain; Crystallography, X-Ray; Enzyme Stability / drug effects; Glutamine / metabolism; Hydrogen Bonding / drug effects; Hydrolysis / drug effects; Hydroxyl Radical / metabolism; Magnesium / metabolism; Models, Molecular; Protein Structure, Tertiary; Structure-Activity Relationship; ras Proteins / chemistry; ras Proteins / metabolism
Source: Web Of Science
Added: August 6, 2018
2009 journal article
A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis
BIOCHEMICAL JOURNAL, 424, 335–345.
author keywords: apoptosis; cancer therapy; conformational switch; co-operative dimer interface; procaspase activation
MeSH headings : Amino Acid Substitution; Apoptosis; Binding Sites / genetics; Blotting, Western; Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Cell Line; Crystallography, X-Ray; Enzyme Activation; Enzyme Precursors / chemistry; Enzyme Precursors / genetics; Enzyme Precursors / metabolism; Humans; Models, Molecular; Mutation; Protein Conformation; Protein Multimerization; Protein Structure, Tertiary; Structure-Activity Relationship; Transfection; X-Linked Inhibitor of Apoptosis Protein / genetics; X-Linked Inhibitor of Apoptosis Protein / metabolism
Source: Web Of Science
Added: August 6, 2018
2009 journal article
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
BIOINFORMATICS, 25(5), 621–627.
MeSH headings : Algorithms; Binding Sites; Crystallography, X-Ray; Internet; Models, Molecular; Protein Conformation; Protein Interaction Mapping; Proteins / chemistry
Source: Web Of Science
Added: August 6, 2018
2009 journal article
Multiple solvent crystal structures of ribonuclease A: An assessment of the method
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76(4), 861–881.
author keywords: organic solvents; solvent mapping; plasticity; hydration; protein binding sites
MeSH headings : Animals; Catalytic Domain; Cattle; Computer Simulation; Crystallography, X-Ray; Models, Molecular; Pancreas / enzymology; Protein Binding; Protein Conformation; Ribonuclease, Pancreatic / chemistry; Ribonuclease, Pancreatic / metabolism; Solvents / chemistry; Solvents / metabolism; Water / chemistry; Water / metabolism
Source: Web Of Science
Added: August 6, 2018
2008 review
Minimizing frustration by folding in an aqueous environment
[Review of ]. Archives of Biochemistry and Biophysics, 469(1), 118–131.
Source: NC State University Libraries
Added: August 6, 2018
2007 journal article
Rapid folding and unfolding of Apaf-1 CARD
JOURNAL OF MOLECULAR BIOLOGY, 369(1), 290–304.
author keywords: caspase recruitment domain; protein folding; folding kinetics; parallel folding channels; sequential mixing stopped-flow
MeSH headings : Apoptotic Protease-Activating Factor 1 / chemistry; Apoptotic Protease-Activating Factor 1 / metabolism; Crystallography, X-Ray; Fluorescence; Kinetics; Models, Biological; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Thermodynamics
Source: Web Of Science
Added: August 6, 2018
2007 journal article
Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf
STRUCTURE, 15(12), 1618–1629.
MeSH headings : Catalysis; Crystallography, X-Ray; Guanosine Triphosphate / metabolism; Hydrolysis; Models, Molecular; Mutation; Protein Conformation; raf Kinases / metabolism; ras Proteins / chemistry; ras Proteins / genetics
Source: Web Of Science
Added: August 6, 2018
2006 journal article
Multiple solvent crystal structures: Probing binding sites, plasticity and hydration
JOURNAL OF MOLECULAR BIOLOGY, 357(5), 1471–1482.
author keywords: elastase; solvent mapping; organic solvents; protein binding sites; multiple solvent crystal structures
MeSH headings : Animals; Binding Sites; Crystallography, X-Ray; Models, Molecular; Molecular Structure; Pancreatic Elastase / chemistry; Pancreatic Elastase / metabolism; Protein Conformation; Solvents; Swine; Water / chemistry
Source: Web Of Science
Added: August 6, 2018
2006 journal article
Role of loop bundle hydrogen bonds in the maturation and activity of (pro) caspase-3
BIOCHEMISTRY, 45(44), 13249–13263.
MeSH headings : Amino Acid Sequence; Base Sequence; Caspase 3 / chemistry; Caspase 3 / metabolism; Crystallography; DNA Primers; Hydrogen Bonding; Hydrogen-Ion Concentration; Hydrolysis; Models, Molecular; Molecular Sequence Data; Protein Conformation; Spectrometry, Fluorescence
Source: Web Of Science
Added: August 6, 2018
2005 journal article
Structural mechanism of oxidative regulation of the phosphatase Cdc25B via an intramolecular disulfide bond
BIOCHEMISTRY, 44(14), 5307–5316.
MeSH headings : Binding Sites; Catalytic Domain; Cell Cycle Proteins / chemistry; Cell Cycle Proteins / metabolism; Crystallization; Disulfides / chemistry; Models, Molecular; Oxidation-Reduction; Protein Conformation; cdc25 Phosphatases / chemistry; cdc25 Phosphatases / metabolism
Source: Web Of Science
Added: August 6, 2018
2004 journal article
Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap
STRUCTURE, 12(11), 2025–2036.
MeSH headings : Amino Acid Sequence; Binding Sites; Catalytic Domain; Crystallography, X-Ray; Guanosine Diphosphate / chemistry; Guanosine Diphosphate / metabolism; Guanosine Triphosphate / analogs & derivatives; Guanosine Triphosphate / chemistry; Guanosine Triphosphate / metabolism; Models, Molecular; Molecular Sequence Data; Protein Conformation; Sequence Homology, Amino Acid; rap GTP-Binding Proteins / chemistry; rap GTP-Binding Proteins / metabolism; ras Proteins / chemistry; ras Proteins / metabolism
Source: Web Of Science
Added: August 6, 2018
2004 journal article
X-ray structural and simulation analysis of a protein mutant: The value of a combined approach
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 55(3), 733–742.
MeSH headings : Bacteriophage T4 / enzymology; Computer Simulation; Crystallography, X-Ray; Enzyme Stability; Histidine / chemistry; Hydrogen Bonding; Models, Molecular; Muramidase / chemistry; Muramidase / genetics; Mutation; Proteins / chemistry; Proteins / genetics; Static Electricity
Source: Web Of Science
Added: August 6, 2018
2003 journal article
Organic solvents order the dynamic switch II in Ras crystals
STRUCTURE, 11(7), 747–751.
MeSH headings : Crystallization; Guanosine Triphosphate / analogs & derivatives; Guanosine Triphosphate / chemistry; Organic Chemicals / chemistry; Solvents / chemistry; ras Proteins / chemistry
Source: Web Of Science
Added: August 6, 2018
2002 review
Protein-water interactions in a dynamic world
[Review of ]. Trends in Biochemical Sciences, 27(4), 203–208.
Source: NC State University Libraries
Added: August 6, 2018
2001 journal article
Proteins in organic solvents
CURRENT OPINION IN STRUCTURAL BIOLOGY, 11(6), 761–764.
MeSH headings : Binding Sites; Catalysis; Crystallography, X-Ray; Protein Conformation; Proteins / chemistry; Solvents / chemistry
Source: Web Of Science
Added: August 6, 2018
