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.

By: B. Kearney n, M. Schwabe*, K. Marcus*, D. Roberts n, M. Dechene n, P. Swartz n, C. Mattos n

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.

By: M. Schwabe*, G. Holzapfel n & C. Mattos*

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.

By: R. Knihtila*, A. Volmar*, F. Meilleur n & C. Mattos*

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.

By: S. Fetics n, H. Guterres*, B. Kearney n, G. Buhrman n, B. Ma*, R. Nussinov*, C. Mattos n

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
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.

By: R. Knihtila*, G. Holzapfel n, K. Weiss*, F. Meilleur n & C. Mattos n

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.

By: B. Kearney n, C. Johnson*, D. Roberts n, P. Swartz n & C. Mattos n

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.

By: J. Walters n, J. Schipper n, P. Swartz n, C. Mattos n & A. Clark n

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.

By: G. Holzapfel n, G. Buhrman n & C. Mattos n

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.

By: K. Gagnon n, S. Biswas n, X. Zhang n, B. Brown n, P. Wollenzien n, C. Mattos n, E. Maxwell n

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.

By: G. Buhrman*, V. Kumar, M. Cirit n, J. Haugh n & C. Mattos*

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.

By: S. Biswas n, G. Buhrman n, K. Gagnon*, C. Mattos n, B. Brown n & E. Maxwell n

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.

By: J. Walters n, P. Swartz n, C. Mattos n & A. Clark n

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.

By: G. Buhrman n, G. Holzapfel*, S. Fetics* & C. Mattos*

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.

By: J. Walters n, C. Pop*, F. Scott*, M. Drag*, P. Swartz n, C. Mattos n, G. Salvesen*, A. Clark n

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.

By: R. Brenke n, D. Kozakov n, G. Chuang n, D. Beglov n, D. Hall n, M. Landon n, C. Mattos n, S. Vajda n

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.

By: M. Dechene n, G. Wink n, M. Smith n, P. Swartz n & C. Mattos n

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.

By: C. Mattos & A. Clark

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.

By: S. Milam n, N. Nicely n, B. Feeney n, C. Mattos n & A. Clark n

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.

By: G. Buhrman n, G. Wink n & C. Mattos n

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.

By: C. Mattos n, C. Bellamacina*, E. Peisach*, A. Pereira*, D. Vitkup*, G. Petsko*, D. Ringe*

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.

By: B. Feeney n, C. Pop n, P. Swartz n, C. Mattos n & A. Clark n

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.

By: G. Buhrman n, B. Parker n, J. Sohn n, J. Rudolph n & C. Mattos n

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.

By: N. Nicely n, J. Kosak n, V. Serrano n & C. Mattos n

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.

By: C. Mattos n, J. Cohen*, D. Green*, B. Tidor* & M. Karplus*

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.

By: G. Buhrman n, V. Serrano n & C. Mattos n

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.

By: C. Mattos

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.

By: C. Mattos n & D. Ringe*

MeSH headings : Binding Sites; Catalysis; Crystallography, X-Ray; Protein Conformation; Proteins / chemistry; Solvents / chemistry
Source: Web Of Science
Added: August 6, 2018