Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-XL

No abstract is available for this paper.

• Publication year

  2011

• Venue

  J. Comput. Aided Mol. Des.

• Publication date

  2011-04-27

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1007/s10822-011-9428-yPMID 21523491
• 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.

• Quantum chemical investigations on intraresidue carbonyl-carbonyl contacts in aspartates of high-resolution protein structures.

  2010cited by this paper
• Peptide drugs to target G protein-coupled receptors.

  2010cited by this paper
• Probing the α‐Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis

  2010cited by this paper
• Bcl-2 inhibitors: small molecules with a big impact on cancer therapy

  2009cited by this paper
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  2009cited by this paper
• The BCL-2 protein family: opposing activities that mediate cell death

  2008cited by this paper
• Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin.

  2008cited by this paper
• Molecular dynamics simulations of an apoliprotein A-I derived peptide in explicit water

  2008cited by this paper
• Anti‐apoptotic Bcl‐XL protein in complex with BH3 peptides of pro‐apoptotic Bak, Bad, and Bim proteins: Comparative molecular dynamics simulations

  2008cited by this paper
• BCL-2 family antagonists for cancer therapy

  2008cited by this paper
• Molecular dynamics studies of alpha-helix stability in fibril-forming peptides.

  2008cited by this paper
• The Universal Protein Resource (UniProt) 2009

  2008cited by this paper
• Molecular dynamics studies of α-helix stability in fibril-forming peptides

  2008cited by this paper
• A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation.

  2008cited by this paper
• Larger than life: Mitochondria and the Bcl-2 family.

  2007cited by this paper
• Examination of the folding of a short alanine-based helical peptide with salt bridges using molecular dynamics simulation.

  2007cited by this paper
• Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures : π...π or lone-pair...π interactions?

  2007cited by this paper
• Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi...pi or lone-pair...pi interactions?

  2007cited by this paper
• BCL-2 Family Proteins: Critical Checkpoints of Apoptotic Cell Death

  2007cited by this paper
• Recognition of GPCRs by Peptide Ligands and Membrane Compartments theory: Structural Studies of Endogenous Peptide Hormones in Membrane Environment

  2006influential reference
• Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study.

  2006cited by this paper
• Differential targeting of prosurvival Bcl-2 proteins by their BH3-only ligands allows complementary apoptotic function.

  2005influential reference
• GROMACS: Fast, flexible, and free

  2005influential reference
• BH3 domains of BH3-only proteins differentially regulate Bax-mediated mitochondrial membrane permeabilization both directly and indirectly.

  2005influential reference
• UCSF Chimera—A visualization system for exploratory research and analysis

  2004cited by this paper
• The Many Roles of Computation in Drug Discovery

  2004cited by this paper
• Amino Acid Propensities are Position-dependent Throughout the Length of α-Helices

  2004cited by this paper
• Solution conformations of wild-type and mutated Bak BH3 peptides via dynamical conformational sampling and implication to their binding to antiapoptotic Bcl-2 proteins

  2004cited by this paper
• The Universal Protein Resource (UniProt)

  2004cited by this paper
• Amino acid propensities are position-dependent throughout the length of alpha-helices.

  2004cited by this paper
• Improved treatment of the protein backbone in empirical force fields.

  2004cited by this paper
• Sequence and helicity requirements for the proapoptotic activity of Bax BH3 peptides.

  2004cited by this paper
• The structure of a Bcl-xL/Bim fragment complex: implications for Bim function.

  2003cited by this paper
• Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics.

  2002cited by this paper
• Occurrence, conformational features and amino acid propensities for the pi-helix.

  2002cited by this paper
• BH3 domains: intracellular death-ligands critical for initiating apoptosis.

  2002cited by this paper
• Life-or-death decisions by the Bcl-2 protein family.

  2001cited by this paper
• Methods of peptide conformation studies.

  2001cited by this paper
• The interrelationships of side-chain and main-chain conformations in proteins.

  2001cited by this paper
• GROMACS 3.0: a package for molecular simulation and trajectory analysis

  2001cited by this paper
• Helix Folding of an Alanine-Based Peptide in Explicit Water

  2001cited by this paper
• Hydrophilic Framework in Proteins?

  2000cited by this paper
• Rationale for Bcl‐XL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies

  2000influential reference
• Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures.

  2000cited by this paper
• Bak BH3 Peptides Antagonize Bcl-xL Function and Induce Apoptosis through Cytochrome c-independent Activation of Caspases*

  1999cited by this paper
• Bcl-2-family proteins: the role of the BH3 domain in apoptosis.

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

  1998cited by this paper
• Parametrization of aliphatic CHn united atoms of GROMOS96 force field

  1998influential reference
• Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search

  1998cited by this paper
• Structure of Bcl-xL-Bak Peptide Complex: Recognition Between Regulators of Apoptosis

  1997influential reference
• LINCS: A linear constraint solver for molecular simulations

  1997cited by this paper
• BH3 Domain of BAD Is Required for Heterodimerization with BCL-XL and Pro-apoptotic Activity*

  1997cited by this paper
• A conserved domain in Bak, distinct from BH1 and BH2, mediates cell death and protein binding functions.

  1995cited by this paper
• Alpha-helix-forming propensities in peptides and proteins.

  1994cited by this paper
• α‐Helix‐forming propensities in peptides and proteins

  1994cited by this paper
• Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

  1992cited by this paper
• Capping and alpha-helix stability.

  1989cited by this paper
• Capping and α-helix stability

  1989cited by this paper
• Molecular dynamics with coupling to an external bath

  1984influential reference
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983cited by this paper
• Interaction Models for Water in Relation to Protein Hydration

  1981cited by this paper

• In silico design of potential Mcl-1 peptide-based inhibitors

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  2022cites this paper
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  2021cites this paper
• Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering

  2021cites this paper
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  2021cites this paper
• A novel computational method to design BH3-mimetic peptide inhibitors that can bind specifically to Mcl-1 or Bcl-XL

  2020cites this paper
• Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-XL: Role of Non-Hot Spot Residues.

  2020cites this paper
• Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide—Mcl1 Complexes

  2020cites this paper
• Computer-aided design of amino acid-based therapeutics: a review

  2018cites this paper
• Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein

  2018cites this paper
• The long unstructured region of Bcl‐xl modulates its structural dynamics

  2017cites this paper
• Binding affinity of pro-apoptotic BH3 peptides for the anti-apoptotic Mcl-1 and A1 proteins: Molecular dynamics simulations of Mcl-1 and A1 in complex with six different BH3 peptides.

  2017cites this paper
• N-H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins.

  2016cites this paper
• Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation.

  2015cites this paper
• A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations

  2014cites this paper
• Progesterone Increases Apoptosis and Inversely Decreases Autophagy in Human Hepatoma HA22T/VGH Cells Treated with Epirubicin

  2014influential citation
• Does there exist an intrinsic relationship between the flexibility and self-assembly of pepfactants?

  2014cites this paper
• ANALYSIS OF THE MONO-, DI-, AND TRINUCLEOTIDE TANDEM REPEATS IN INF2 OF GLOMERULAR PODOCYTE

  2013cites this paper
• Running title: Pro-survival effect of P4 during bovine oocyte maturation

  2013cites this paper
• Computational peptidology: a new and promising approach to therapeutic peptide design.

  2013cites this paper
• Poxvirus antagonism of innate immunity by Bcl-2 fold proteins.

  2013cites this paper
• Structural Biology: Modeling applications and techniques at a glance

  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2013cites this paper
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  2012cites this paper
• Computational modeling and simulation of the Bcl-2 family: paving the way for rational drug design.

  2012cites this paper
• NMR solution structure of a photoswitchable apoptosis activating Bak peptide bound to Bcl-xL.

  2012cites this paper