In silico modeling of pH-optimum of protein-protein binding (Q39037535)

8 September 2017

In silico modeling of pH-optimum of protein-protein binding (English)

1 reference

8 September 2017

1 reference

Rooplekha C Mitra

1 reference

8 September 2017

Zhe Zhang

series ordinal

1 reference

8 September 2017

Emil Alexov

series ordinal

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8 September 2017

language of work or name

English

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publication date

22 December 2010

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8 September 2017

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8 September 2017

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8 September 2017

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8 September 2017

925-936

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Adaptations of proteins to cellular and subcellular pH

8 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Evidence for the adaptation of protein pH-dependence to subcellular pH.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Protein-protein interaction as a predictor of subcellular location

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Menin interacts with IQGAP1 to enhance intercellular adhesion of beta-cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Very fast prediction and rationalization of pKa values for protein-ligand complexes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Tissue specificity of mitochondrial glutamate pathways and the control of metabolic homeostasis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Calculating pH and salt dependence of protein-protein binding

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Structural analysis of the synaptic protein neuroligin and its beta-neurexin complex: determinants for folding and cell adhesion

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

The regulation of the B-cell gene expression programme by Pax5.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Modeling electrostatic effects in proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Prediction of physical protein-protein interactions

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Charge sequence coding in statistical modeling of unfolded proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Protein-protein docking predictions for the CAPRI experiment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Site-specific contributions to the pH dependence of protein stability

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Electrostatics in protein binding and function

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Novel approaches to controlling transcription.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

BRENDA: a resource for enzyme data and metabolic information

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Electrostatic aspects of protein-protein interactions.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Principles of protein-protein interactions

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH dependence of the stability of barstar to chemical and thermal denaturation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

In silico identification of functional protein interfaces

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Interactions of LSECtin and DC-SIGN/DC-SIGNR with viral ligands: Differential pH dependence, internalization and virion binding.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Diabetes-associated mitochondrial DNA mutation A3243G impairs cellular metabolic pathways necessary for beta cell function.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH-dependent processes in proteins.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

On the pH-optimum of activity and stability of proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Electrostatic rate enhancement and transient complex of protein-protein association

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Electrostatic properties of protein-protein complexes

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Flavine-protein interactions in flavoenzymes. The pH dependence of the binding of flavine mononucleotide and riboflavine to Azotobacter flavodoxin

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Mechanisms of inhibition of zinc-finger transcription factors by selenium compounds ebselen and selenite.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH Dependence of peptidylglycine monooxygenase. Mechanistic implications of Cu-methionine binding dynamics.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Insights into protein-protein interfaces using a Bayesian network prediction method

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Controlling gene expression in Drosophila using engineered zinc finger protein transcription factors.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Statistical analysis and prediction of protein-protein interfaces

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

An evolution based classifier for prediction of protein interfaces without using protein structures

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

PIBASE: a comprehensive database of structurally defined protein interfaces

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Association of hormone replacement therapy to estrogen and progesterone receptor status in invasive breast carcinoma

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Human NK cells express Fc receptors for IgA which mediate signal transduction and target cell killing.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

A protein-protein docking benchmark.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Structural characterisation and functional significance of transient protein-protein interactions

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

On the pH dependence of protein stability.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3213863

pH-Dependent Conformational Stability of the Ribotoxin α-Sarcin and Four Active Site Charge Substitution Variants†

4 November 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22931

Protein-protein binding is often associated with changes in protonation state

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22931

Urea denaturation of barnase: pH dependence and characterization of the unfolded state

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22931

A Calorimetric Study of the Thermal Stability of Barstar and Its Interaction with Barnase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22931

pH Dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: Application to 2′GMP/3′GMP binding to ribonuclease T1 and implications for catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22931

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

21 January 2018

1 reference

12 December 2020

Biophysical characterization of the interaction of the beta-lactamase TEM-1 with its protein inhibitor BLIP

1 reference

12 December 2020

Subcellular pH and predicted pH-dependent features of proteins

1 reference

12 December 2020

Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering

1 reference

12 December 2020

Dissection of the pH dependence of inhibitor binding energetics for an aspartic protease: direct measurement of the protonation states of the catalytic aspartic acid residues

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22931

1 reference

8 September 2017

1 reference

8 September 2017

PubMed publication ID

21287623

1 reference