Physical nature of intermolecular interactions within cAMP-dependent protein kinase active site: differential transition state stabilization in phosphoryl transfer reaction.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Journal of Physical Chemistry B

• Publication date

  2008-08-23

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1021/jp8040633PMID 18720966
• 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.

• De Novo Computational Design of Retro-Aldol Enzymes

  2008cited by this paper
• Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions

  2007cited by this paper
• Enzymatic Transition State Theory and Transition State Analogue Design*

  2007cited by this paper
• The field theoretical study of chemical interaction in terms of the Rigged QED: new reactivity indices

  2007cited by this paper
• How does activation loop phosphorylation modulate catalytic activity in the cAMP‐dependent protein kinase: A theoretical study

  2006cited by this paper
• Electrostatic basis for enzyme catalysis.

  2006cited by this paper
• Mechanisms and free energies of enzymatic reactions.

  2006cited by this paper
• How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study.

  2005cited by this paper
• Conformational dependence of a protein kinase phosphate transfer reaction

  2004cited by this paper
• Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases.

  2004cited by this paper
• Structure of a human inositol 1,4,5-trisphosphate 3-kinase: substrate binding reveals why it is not a phosphoinositide 3-kinase.

  2004cited by this paper
• Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.

  2004cited by this paper
• Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations.

  2004cited by this paper
• The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations.

  2003cited by this paper
• Flexible structure alignment by chaining aligned fragment pairs allowing twists

  2003cited by this paper
• Computational Approaches to Biochemical Reactivity

  2002cited by this paper
• Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism.

  2002cited by this paper
• Dynamics of cAMP-dependent protein kinase.

  2001cited by this paper
• Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase.

  2001cited by this paper
• Kinetic and catalytic mechanisms of protein kinases.

  2001cited by this paper
• Serine-53 at the tip of the glycine-rich loop of cAMP-dependent protein kinase: role in catalysis, P-site specificity, and interaction with inhibitors.

  2000cited by this paper
• Influence of key residues on the reaction mechanism of the cAMP‐dependent protein kinase

  1999cited by this paper
• The catalytic subunit of cAMP-dependent protein kinase: prototype for an extended network of communication.

  1999cited by this paper
• Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A.

  1998cited by this paper
• Role of the Glycine Triad in the ATP-binding Site of cAMP-dependent Protein Kinase*

  1997cited by this paper
• VMD: visual molecular dynamics.

  1996cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• cAMP‐dependent protein kinase: Crystallographic insights into substrate recognition and phosphotransfer

  1994cited by this paper
• 2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.

  1993cited by this paper
• Rational scanning mutagenesis of a protein kinase identifies functional regions involved in catalysis and substrate interactions.

  1991cited by this paper
• Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family members.

  1991cited by this paper
• Catalytic activity of aminoacyl tRNA synthetases and its implications for the origin of life. I. Aminoacyl adenylate formation in tyrosyl tRNA synthetase

  1991cited by this paper
• cAMP‐dependent protein kinase: prototype for a family of enzymes

  1988cited by this paper
• Chemical mechanism of the adenosine cyclic 3',5'-monophosphate dependent protein kinase from pH studies.

  1987cited by this paper
• Magnetic resonance and kinetic studies of the manganese(II) ion and substrate complexes of the catalytic subunit of adenosine 3',5'-monophosphate dependent protein kinase from bovine heart.

  1979cited by this paper

• How a second Mg 2+ ion affects the 3 phosphoryl transfer mechanism in a 4 protein kinase: a computational study 5

  2020cites this paper
• Extreme Catalytic Power of Ketosteroid Isomerase Related to the Reversal of Proton Dislocations in Hydrogen-Bond Network

  2020cites this paper
• Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields

  2020cites this paper
• QM/MM calculations and MD simulations on acetate CoA-transferase to reveal its catalytic mechanism and illuminate the role of residue Asn347

  2018cites this paper
• Globally Optimal Catalytic Fields - Inverse Design of Abstract Embeddings for Maximum Reaction Rate Acceleration.

  2018cites this paper
• Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants.

  2017cites this paper
• Predicting substituent effects on activation energy changes by static catalytic fields

  2017cites this paper
• Fragment molecular orbital study of the cAMP-dependent protein kinase catalyzed phosphoryl transfer: a comparison with the differential transition state stabilization method.

  2016cites this paper
• Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure.

  2016cites this paper
• Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study

  2015cites this paper
• A simplified electrostatic model for hydrolase catalysis.

  2015cites this paper
• A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant

  2014cites this paper
• Metal-Free cAMP-Dependent Protein Kinase Can Catalyze Phosphoryl Transfer

  2014cites this paper
• Physical Nature of Fatty Acid Amide Hydrolase Interactions with Its Inhibitors: Testing a Simple Nonempirical Scoring Model.

  2014cites this paper
• Theoretical studies of cyclic adenosine monophosphate dependent protein kinase: native enzyme and ground-state and transition-state analogues.

  2014cites this paper
• Physical nature of intermolecular interactions in [BMIM][PF6] ionic liquid.

  2014cites this paper
• Unique Kinase Catalytic Mechanism of AceK with a Single Magnesium Ion

  2013influential citation
• Nonempirical energetic analysis of reactivity and covalent inhibition of fatty acid amide hydrolase.

  2013cites this paper
• Functional analyses of pSer and pThr binding domains

  2013cites this paper
• Phosphoryl transfer by protein kinase A is captured in a crystal lattice.

  2013cites this paper
• Bioinformatics and Computational Biology in Poland

  2013cites this paper
• How calcium inhibits the magnesium‐dependent kinase gsk3β: A molecular simulation study

  2013cites this paper
• Hyperconjugation-mediated solvent effects in phosphoanhydride bonds.

  2012cites this paper
• Dissection of the difference between the group I metal ions in inhibiting GSK3β: a computational study.

  2011cites this paper
• Protein kinase biochemistry and drug discovery.

  2011cites this paper
• Structural Characterisation of Human Kinases using a Library-Based Construct Screening Approach

  2009cites this paper