Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations.

No abstract is available for this paper.

• Publication year

  2001

• Venue

  Biopolymers

• Publication date

  2001-09-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1002/1097-0282(200109)59:3<145::AID-BIP1014>3.0.CO;2-ZPMID 11391564
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• An Interpretation of Small-Ion Effects on the Electrostatics of the λ Repressor DNA Complex

  2000cited by this paper
• Contribution of surface salt bridges to protein stability.

  2000cited by this paper
• Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers

  2000cited by this paper
• Contribution of cation-pi interactions to the stability of protein-DNA complexes.

  2000cited by this paper
• Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges.

  2000cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Does the elimination of ion pairs affect the thermal stability of cold shock protein from the hyperthermophilic bacterium Thermotoga maritima?

  1999cited by this paper
• Ewald artifacts in computer simulations of ionic solvation and ion–ion interaction: A continuum electrostatics study

  1999cited by this paper
• Electrostatic contributions to the stability of hyperthermophilic proteins.

  1999cited by this paper
• Comparative stability analysis of the thyroid transcription factor 1 and Antennapedia homeodomains: evidence for residue 54 in controlling the structural stability of the recognition helix.

  1999cited by this paper
• Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study.

  1999cited by this paper
• The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains.

  1999cited by this paper
• Molecular dynamics simulations of biomolecules: long-range electrostatic effects.

  1999cited by this paper
• Prediction of stability changes upon single-site mutations using database-derived potentials

  1999cited by this paper
• The hyperthermostable indoleglycerol phosphate synthase from Thermotoga maritima is destabilized by mutational disruption of two solvent-exposed salt bridges.

  1999cited by this paper
• Target genes of homeodomain proteins.

  1999cited by this paper
• Site-directed Mutations in the vnd/NK-2 Homeodomain

  1998cited by this paper
• Structural classification of αββ and ββα supersecondary structure units in proteins

  1998cited by this paper
• The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins.

  1998cited by this paper
• Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins.

  1998cited by this paper
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998cited by this paper
• Anatomy by computer experiment of the exchange of a water molecule buried in human apolipoprotein E.

  1998cited by this paper
• Electrostatic effects in homeodomain-DNA interactions.

  1997cited by this paper
• Energetics of folding and DNA binding of the MAT alpha 2 homeodomain.

  1997cited by this paper
• Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity.

  1997cited by this paper
• Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.

  1997cited by this paper
• Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence.

  1997cited by this paper
• Structural role of a buried salt bridge in the 434 repressor DNA-binding domain.

  1996cited by this paper
• Structural classification of HTH DNA-binding domains and protein-DNA interaction modes.

  1996cited by this paper
• Automatic classification and analysis of alpha alpha-turn motifs in proteins.

  1996cited by this paper
• Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials.

  1996cited by this paper
• Covariation of residues in the homeodomain sequence family

  1995cited by this paper
• Solution structure of the Oct-1 POU homeodomain determined by NMR and restrained molecular dynamics

  1995cited by this paper
• High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA.

  1995cited by this paper
• Are buried salt bridges important for protein stability and conformational specificity?

  1995cited by this paper
• Classical electrostatics in biology and chemistry.

  1995cited by this paper
• Do salt bridges stabilize proteins? A continuum electrostatic analysis

  1994cited by this paper
• Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary structure study by NMR.

  1994cited by this paper
• Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in λ repressor

  1994cited by this paper
• Satisfying hydrogen bonding potential in proteins.

  1994cited by this paper
• Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain.

  1994cited by this paper
• Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules.

  1994cited by this paper
• Analysis of the conformation and stability of rat TTF‐1 homeodomain by circular dichroism

  1994cited by this paper
• Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2.

  1994cited by this paper
• Identification of short turn motifs in proteins using sequence and structure fingerprints

  1994cited by this paper
• Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.

  1993cited by this paper
• The X‐ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding.

  1993cited by this paper
• The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding.

  1993cited by this paper
• Structural study of rat thyroid transcription factor 1 homeodomain (TTF‐1 HD) by nuclear magnetic resonance

  1993cited by this paper
• Cutoff size does strongly influence molecular dynamics results on solvated polypeptides.

  1992cited by this paper
• Electrostatic effects on protein stability: Current Opinion in Structural Biology 1992, 2:40…-45

  1992cited by this paper
• Contributions of engineered surface salt bridges to the stability of T4 lysozyme determined by directed mutagenesis.

  1991cited by this paper
• Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons

  1991cited by this paper
• Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions.

  1991cited by this paper
• Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions.

  1991cited by this paper
• Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles.

  1990cited by this paper
• pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme.

  1990cited by this paper
• Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.

  1990cited by this paper
• Computer simulations of liquid water: treatment of long-range interactions

  1990cited by this paper
• Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design.

  1987cited by this paper
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983cited by this paper
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

  1983cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper
• A discussion of the solution for the best rotation to relate two sets of vectors

  1978cited by this paper
• A gene complex controlling segmentation in Drosophila

  1978cited by this paper
• Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes

  1977cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper
• Sequence-specific recognition of double helical nucleic acids by proteins.

  1976cited by this paper
• Conformational equilibria in -and -chymotrypsin. The energetics and importance of the salt bridge.

  1972cited by this paper
• Sequence-specific Recognition of Double Helical Nucleic Acids by Proteins (base Pairs/hydrogen Bonding/recognition Fidelity/ion Binding)

  year unknowncited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• Discovery of novel IDO1/TDO2 dual inhibitors: a consensus Virtual screening approach with molecular dynamics simulations, and binding free energy analysis

  2024cites this paper
• DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates

  2015cites this paper
• Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain

  2013cites this paper
• The role of electrostatic interactions in the stability and structural integrity of human CLIC1

  2012cites this paper
• Decoding transcriptional regulatory interactions.

  2006cites this paper
• Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome.

  2005cites this paper
• Cation-pi/H-bond stair motifs at protein-DNA interfaces.

  2002cites this paper
• The [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1 peptide retains the specific Arg(-1)-Asp8 salt bridge but reveals discrepancies between NMR data and molecular dynamics simulations.

  2002cites this paper