(Q51822136)

13 April 2018

title

A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. (English)

1 reference

13 April 2018

main subject

protein design

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computational biology

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Katrina L Schweiker

1

1 reference

13 April 2018

George I Makhatadze

series ordinal

2

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13 April 2018

language of work or name

English

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publication date

1 January 2009

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13 April 2018

published in

Methods in Enzymology

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13 April 2018

volume

454

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13 April 2018

page(s)

175-211

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13 April 2018

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

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Electrostatic contributions to the stability of halophilic proteins

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7 January 2021

Bacterial cold-shock proteins

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7 January 2021

Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices

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7 January 2021

Thermodynamic analysis of helix-engineered forms of the activation domain of human procarboxypeptidase A2.

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Structural interpretation of pH and salt-dependent processes in proteins with computational methods

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7 January 2021

The three-dimensional structure of human procarboxypeptidase A2. Deciphering the basis of the inhibition, activation and intrinsic activity of the zymogen

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7 January 2021

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

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7 January 2021

Directed evolution of a thermostable esterase.

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7 January 2021

Empirical parametrization of pK values for carboxylic acids in proteins using a genetic algorithm.

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7 January 2021

Structural analysis of the N- and C-termini in a peptide with consensus sequence

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7 January 2021

Recombinant phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima: catalytic, spectral and thermodynamic properties

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7 January 2021

Role of the charge-charge interactions in defining stability and halophilicity of the CspB proteins

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7 January 2021

Heat and cold denaturation of phosphoglycerate kinase (interaction of domains).

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7 January 2021

Thermodynamics of barnase unfolding

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7 January 2021

Cold denaturation of staphylococcal nuclease

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7 January 2021

Increasing protein stability by altering long-range coulombic interactions

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7 January 2021

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7 January 2021

Cooperativity of complex salt bridges

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7 January 2021

Directed evolution by accumulating tailored mutations: thermostabilization of lactate oxidase with less trade-off with catalytic activity

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7 January 2021

A thermodynamic comparison of mesophilic and thermophilic ribonucleases H.

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7 January 2021

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7 January 2021

Strength and co-operativity of contributions of surface salt bridges to protein stability

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7 January 2021

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7 January 2021

Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme

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7 January 2021

Thermal versus guanidine-induced unfolding of ubiquitin. An analysis in terms of the contributions from charge-charge interactions to protein stability

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7 January 2021

Cold denaturation of ubiquitin

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7 January 2021

Salt effects on ionization equilibria of histidines in myoglobin

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7 January 2021

Some factors in the interpretation of protein denaturation

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7 January 2021

Computational thermostabilization of an enzyme

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7 January 2021

Native protein sequences are close to optimal for their structures

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

pKaValues and the pH Dependent Stability of the N-Terminal Domain of L9 as Probes of Electrostatic Interactions in the Denatured State. Differentiation between Local and Nonlocal Interactions†

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7 January 2021

Evaluation of the energetic contribution of an ionic network to beta-sheet stability

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

De novo design of the hydrophobic core of ubiquitin

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7 January 2021

Structure of a Fibronectin Type III Domain from Tenascin Phased by MAD Analysis of the Selenomethionyl Protein

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7 January 2021

Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer.

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7 January 2021

Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein

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7 January 2021

Heat capacity changes upon burial of polar and nonpolar groups in proteins

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7 January 2021

Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior

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7 January 2021

Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface

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7 January 2021

Both helical propensity and side-chain hydrophobicity at a partially exposed site in alpha-helix contribute to the thermodynamic stability of ubiquitin.

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7 January 2021

Major cold shock proteins, CspA from Escherichia coli and CspB from Bacillus subtilis, interact differently with single-stranded DNA templates

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7 January 2021

Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition

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7 January 2021

Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA. Importance of the T base content and position within the template

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7 January 2021

Thermodynamics Of alpha-Helix Formation

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7 January 2021

Thermodynamics of unfolding of the all beta-sheet protein interleukin-1 beta.

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7 January 2021

Thermodynamics of BPTI folding

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7 January 2021

Contribution of surface salt bridges to protein stability: guidelines for protein engineering

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7 January 2021

Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions.

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7 January 2021

Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor

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7 January 2021

Electrostatics significantly affect the stability of designed homeodomain variants

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7 January 2021

Comparative protein structure modeling of genes and genomes

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7 January 2021

Calculation of electrostatic interactions in proteins

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7 January 2021

Stabilization and destabilization of protein structure by charge interactions

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7 January 2021

T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.

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7 January 2021

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

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7 January 2021

Effect of active site residues in barnase on activity and stability

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7 January 2021

Sidechain interactions in parallel beta sheets: the energetics of cross-strand pairings

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7 January 2021

Functional expression and stabilization of horseradish peroxidase by directed evolution in Saccharomyces cerevisiae

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7 January 2021

Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: a structural and dynamic analysis.

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7 January 2021

High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides

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7 January 2021

An inverse correlation between loop length and stability in a four-helix-bundle protein.

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7 January 2021

Analysis of the interaction between charged side chains and the alpha-helix dipole using designed thermostable mutants of phage T4 lysozyme

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7 January 2021

pKA values of carboxyl groups in the native and denatured states of barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds

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7 January 2021

Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin

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7 January 2021

Determination and analysis of urea and guanidine hydrochloride denaturation curves

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7 January 2021

Charge-charge interactions influence the denatured state ensemble and contribute to protein stability

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7 January 2021

pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1.

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7 January 2021

Forces contributing to the conformational stability of proteins

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7 January 2021

Two exposed amino acid residues confer thermostability on a cold shock protein

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7 January 2021

Electrostatic stabilization of a thermophilic cold shock protein

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7 January 2021

Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins

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7 January 2021

How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin.

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7 January 2021

Review: protein design--where we were, where we are, where we're going.

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7 January 2021

Amino-acid substitutions in a surface turn modulate protein stability

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7 January 2021

Cold denaturation of proteins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Hydrolytic activity of muscle acyl phosphatase on 3-phosphoglyceryl phosphate.

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7 January 2021

Aromatic acyl phosphates as substrates of acyl phosphatase

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7 January 2021

Some thermodynamic implications for the thermostability of proteins

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7 January 2021

Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect.

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7 January 2021

On the relationship between thermal stability and catalytic power of enzymes

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7 January 2021

Nucleotide binding to the G12V-mutant of Cdc42 investigated by X-ray diffraction and fluorescence spectroscopy: Two different nucleotide states in one crystal

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Surface electrostatic interactions contribute little of stability of barnase

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

To charge or not to charge?

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

What are the dielectric "constants" of proteins and how to validate electrostatic models?

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability

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7 January 2021

The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

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7 January 2021

A relationship between protein stability and protein function

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Rational Modification of Protein Stability by the Mutation of Charged Surface Residues†

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7 January 2021

Computational protein design

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https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Protein stability and surface electrostatics: a charged relationship.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Contribution of surface salt bridges to protein stability

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Cumulative site-directed charge-change replacements in bacteriophage T4 lysozyme suggest that long-range electrostatic interactions contribute little to protein stability

1 reference

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7 January 2021

Hydrogen bonds and the pH dependence of ovomucoid third domain stability

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices

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7 January 2021

Contribution of the 30/36 hydrophobic contact at the C-terminus of the alpha-helix to the stability of the ubiquitin molecule

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7 January 2021

Crystal structure of common type acylphosphatase from bovine testis

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7 January 2021

Importance of two buried salt bridges in the stability and folding pathway of barnase.

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7 January 2021

Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa.

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7 January 2021

Relation between stability, dynamics and enzyme activity in 3-phosphoglycerate kinases from yeast and Thermus thermophilus

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7 January 2021

Experimental analysis of the Schellman motif

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7 January 2021

Structure of ubiquitin refined at 1.8 A resolution

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7 January 2021

Computer simulations of enzyme catalysis: methods, progress, and insights

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7 January 2021

pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Thermodynamics of ubiquitin unfolding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Stabilization of the cold shock protein CspB from Bacillus subtilis by evolutionary optimization of Coulombic interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Evolutionary protein stabilization in comparison with computational design

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

In vitro evolution of a hyperstable Gbeta1 variant

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Electrostatic contributions to the stability of hyperthermophilic proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

On the calculation of pKas in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Energetics of ribonuclease T1 structure.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Residual Electrostatic Effects in the Unfolded State of the N-Terminal Domain of L9 Can Be Attributed to Nonspecific Nonlocal Charge−Charge Interactions†

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Simple electrostatic model improves designed protein sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

pH-dependent processes in proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

Studies on protein stability with T4 lysozyme

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2808%2903807-X

7 January 2021

10.1016/S0076-6879(08)03807-X

Identifiers

DOI

1 reference

13 April 2018

1 reference

13 April 2018