(Q73403638)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

title

Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

author name string

Saito M

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

Sarai A

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

publication date

1 February 2000

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

volume

38

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

page(s)

197-209

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants

3 November 2019

cites work

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Increasing the thermostability of the neutral proteinase of Bacillus stearothermophilus by improvement of internal hydrogen-bonding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Some factors in the interpretation of protein denaturation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Hydrophobic bonding and accessible surface area in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Structural invariants in protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Areas, volumes, packing and protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Simulation analysis of the stability mutant R96H of T4 lysozyme.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Probing protein stability with unnatural amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Free energy simulations: the meaning of the individual contributions from a component analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Decomposition of the Free Energy of a System in Terms of Specific Interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Decomposition of interaction free energies in proteins and other complex systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Thermal stability of the DNA-binding domain of the Myb oncoprotein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Shape and energetics of a cavity in c-Myb probed by natural and non-natural amino acid mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Characterization of the internal motions of Escherichia coli ribonuclease HI by a combination of 15N-NMR relaxation analysis and molecular dynamics simulation: examination of dynamic models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Solvent-accessible surfaces of proteins and nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Internal cavities and buried waters in globular proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Analysis of the steric strain in the polypeptide backbone of protein molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Evidence for strained interactions between side-chains and the polypeptide backbone.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Crystal structural analysis of mutations in the hydrophobic cores of barnase

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Convergence Properties of Free Energy Calculations: .alpha.-Cyclodextrin Complexes as a Case Study

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291097-0134%2820000201%2938%3A2%3C197%3A%3AAID-PROT8%3E3.0.CO%3B2-B

10.1002/(SICI)1097-0134(20000201)38:2<197::AID-PROT8>3.0.CO;2-B

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10656266%20AND%20SRC:MED&resulttype=core&format=json

3 November 2019

1 reference