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
TL;DR: A previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) is presented and used together with published structures to illustrate the capabilities of DRoP, a flexible tool developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. (via Semantic Scholar)
UN Sustainable Development Goal Categories
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*

UN Sustainable Development Goal Categories
8. Decent Work and Economic Growth (OpenAlex)
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
TL;DR: The use of a single crystal of the small GTPase Ras to collect three neutron data sets is reported, enabling an in crystallo titration study using NPC, which will allow the analysis of allosteric water-mediated communication networks across the molecule, particularly regarding Cys118 and three tyrosine residues central to these networks. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
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
TL;DR: Crystallography, solution scattering, dynamics, membranes, labeling and imaging, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods are examined. (via Semantic Scholar)
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
TL;DR: In addition to local perturbations on Ras, RasQ61L has substantial long-range effects on the Ras allosteric lobe and on Raf-RBD, which is essential for the activation of the Raf kinase domain through a currently unknown mechanism. (via Semantic Scholar)
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
TL;DR: The neutron crystal structure of RAS bound to the GTP analogue GppNHp shows a protonated γ-phosphate at physiological pH, which counters the notion that the phosphate groups of GTP are fully deprotonated at the start of the hydrolysis reaction. (via Semantic Scholar)
UN Sustainable Development Goal Categories
8. Decent Work and Economic Growth (OpenAlex)
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
TL;DR: The program Detection of Related Solvent Positions (DRoP) is presented for crystallographic water analysis on protein surfaces and used to study Ras, where it was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras. (via Semantic Scholar)
UN Sustainable Development Goal Categories
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
TL;DR: The results demonstrate that considering allosteric inhibition of caspase 3 as a shift between discrete ‘off-state’ or ‘on- state’ conformations is insufficient and requires the representation of an ensemble of inactive states and shows that subtle structural changes lead to the population of the inactive ensemble. (via Semantic Scholar)
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
TL;DR: It is shown with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the "on" state, where the active site appears to be poised for catalysis (calcium acetate), or to what (via Semantic Scholar)
UN Sustainable Development Goal Categories
8. Decent Work and Economic Growth (OpenAlex)
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
TL;DR: The archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
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
TL;DR: The allosteric switch is linked to the control of signaling in the Ras/Raf/MEK/ERK pathway, supporting a GTPase-activating protein-independent model for duration of the Ras-Raf complex. (via Semantic Scholar)
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
TL;DR: Comp comparative sequence analysis indicated a distinct evolutionary position between Archaea and Eukarya, and the Giardia 15.5kD protein occupies a unique position in the evolution of this box C/D RNP core protein retaining structural and functional features characteristic of both archaeal L7Ae and higher eukaryotic 15. (via Semantic Scholar)
UN Sustainable Development Goal Categories
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
TL;DR: Results suggest E246 and K242 are important in procaspase-3 for their interaction with neighboring residues, not with one another, and formation of the K242-E246 salt bridge in caspases3 is needed for an accurate, stable conformation of loop L4 and proper active site formation in the mature enzyme. (via Semantic Scholar)
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 n, S. Fetics n & C. Mattos n

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
TL;DR: This structure suggests a direct catalytic role for Q61 where it interacts with a water molecule that bridges one of the γ-phosphate oxygen atoms to the hydroxyl group of Y32 to stabilize the transition state of the hydrolysis reaction. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
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
TL;DR: It is shown that low concentrations of the pseudo-activated procaspase-3 kill mammalian cells rapidly and, importantly, this protein is not cleaved nor is it inhibited efficiently by the endogenous regulator XIAP (X-linked inhibitor of apoptosis). (via Semantic Scholar)
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
TL;DR: The FTMAP algorithm is developed that performs global search of the entire protein surface for regions that bind a number of small organic probe molecules and shows that the major CSs trace out the shape of the first approved renin inhibitor, aliskiren. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
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
TL;DR: Comparison of the MSCS structures with inhibitor‐bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot‐spots in the active site. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
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
TL;DR: Examination of the equilibrium and kinetic folding of the CARD of Apaf-1 (apoptotic protease activating factor 1), which consists of 97 amino acid residues, at pH 6 and pH 8 showed that the native ensemble is formed rapidly upon refolding, in contrast to other CARDs in which folding appears to be dominated by formation of kinetic traps. (via Semantic Scholar)
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
TL;DR: The results suggest that Y32 and a water molecule bridging it to the gamma-phosphate in the wild-type structure play a role in GTP hydrolysis in lieu of the Arg finger in the absence of GAP. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
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
TL;DR: The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design. (via Semantic Scholar)
UN Sustainable Development Goal Categories
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
TL;DR: It is shown that replacing the residues affects the activity of the procaspase as well as the mature caspase, with D169A and E167A replacements having the largest effects. (via Semantic Scholar)
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
TL;DR: A crystallographic time course is obtained revealing the structural rearrangements that occur in the P-loop as the enzyme goes from its apo state, through the sulfenic intermediate, to the stable disulfide. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
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
TL;DR: Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction, one of which is adjacent to switch I and the other is modulated by switch II and is obstructed in RAl-GDP. (via Semantic Scholar)
UN Sustainable Development Goal Categories
8. Decent Work and Economic Growth (OpenAlex)
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 n

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
TL;DR: Comparisons between the experimental and calculated values for the difference between the free energy of denaturation of the mutant and the wild type show the importance of the combined use of simulations and crystallography for interpreting the effects of mutations on the energetics of the system. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
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
TL;DR: The results suggest that hydrophobic solvents can be used in general to order short biologically relevant segments of disordered regions in protein crystals by favoring H-bonding interactions between atoms that are highly solvated and mobile in aqueous solution. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
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
TL;DR: The demonstration that it is possible to qualitatively rank the affinities of protein binding sites for a given organic solvent using the multiple solvent crystal structures method. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

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