Why nature really chose phosphate

Determinants of Reactivity and Selectivity in Soluble Epoxide Hydrolase from Quantum Mechanics/Molecular Mechanics Modeling

(2012) Richard Lonsdale et al.   BIOCHEMISTRY

Energy phase shift as mechanism for catalysis

(2012) Tamás Beke-Somfai et al.   CHEMICAL PHYSICS LETTERS

Catalytic promiscuity inPseudomonas aeruginosaarylsulfatase as an example of chemistry-driven protein evolution

(2012) Jinghui Luo et al.   FEBS LETTERS

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling

(2012) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic Insights into the Hydrolysis of a Nucleoside Triphosphate Model in Neutral and Acidic Solution

(2012) Rachel Glaves et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression

(2012) J. M. Drake et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations

(2012) Serdal Kirmizialtin et al.   STRUCTURE

Kinetic Consequences of Replacing the Internucleotide Phosphorus Atoms in DNA with Arsenic

(2011) Mostafa I. Fekry et al.   ACS Chemical Biology

Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

(2011) Kin-Yiu Wong et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis

(2011) Jonathan K. Lassila et al.   Annual Review of Biochemistry

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

(2011) Shina C.L. Kamerlin et al.   Annual Review of Physical Chemistry

Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis

(2011) Gordon G. Hammes et al.   BIOCHEMISTRY

A mechanism of catalyzed GTP hydrolysis by Ras protein through magnesium ion

(2011) Qiang Lu et al.   CHEMICAL PHYSICS LETTERS

Insights into Ligand–Protein Binding from Local Mechanical Response

(2011) Jagdish Suresh Patel et al.   Journal of Chemical Theory and Computation

Methyl Phosphate Dianion Hydrolysis in Solution Characterized by Path Collective Variables Coupled with DFT-Based Enhanced Sampling Simulations

(2011) Davide Branduardi et al.   Journal of Chemical Theory and Computation

Directed Evolution of Sulfotransferases and Paraoxonases by Ancestral Libraries

(2011) Uria Alcolombri et al.   JOURNAL OF MOLECULAR BIOLOGY

High-Resolution Analysis of Zn2+ Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography

(2011) Elena Bobyr et al.   JOURNAL OF MOLECULAR BIOLOGY

Theoretical Comparison ofp-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

(2011) Shina Caroline Lynn Kamerlin   JOURNAL OF ORGANIC CHEMISTRY

QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

(2011) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into the Phosphoryl Transfer Mechanism of Cyclin-Dependent Protein Kinases from ab Initio QM/MM Free-Energy Studies

(2011) Gregory K. Smith et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Kinetics and product distribution of p-nitrophenyl phosphate dianion solvolysis in ternary DMSO/alcohol/water mixtures are compatible with metaphosphate formation

(2011) F. S. Lima et al.   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

Catalytic Proficiency: The Extreme Case of S–O Cleaving Sulfatases

(2011) David R. Edwards et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Promiscuity in Alkaline Phosphatase Superfamily. Unraveling Evolution through Molecular Simulations

(2011) Violeta López-Canut et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

QM/MM Analysis Suggests That Alkaline Phosphatase (AP) and Nucleotide Pyrophosphatase/Phosphodiesterase Slightly Tighten the Transition State for Phosphate Diester Hydrolysis Relative to Solution: Implication for Catalytic Promiscuity in the AP Superfamily

(2011) Guanhua Hou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis

(2011) Shina C. L. Kamerlin et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Targeting EGFR and VEGF(R) pathway cross-talk in tumor survival and angiogenesis

(2011) Annette K. Larsen et al.   PHARMACOLOGY & THERAPEUTICS

Multiscale modeling of biological functions

(2011) Shina Caroline Lynn Kamerlin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Torsional elasticity and energetics of F1-ATPase

(2011) J. Czub et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

(2011) S. Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome

(2011) A. J. Adamczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

(2011) A. J. Adamczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Double-lock ratchet mechanism revealing the role of  SER-344 in FoF1 ATP synthase

(2011) T. Beke-Somfai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prechemistry versus preorganization in DNA replication fidelity

(2011) B. Ram Prasad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: A comparison to analogous phosphatases

(2011) Jinghui Luo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis

(2011) Zhao Qin Bao et al.   STRUCTURE

The empirical valence bond model: theory and applications

(2011) Shina C. L. Kamerlin et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Unraveling the Structure of the Ribosome (Nobel Lecture)

(2010) V. Ramakrishnan   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hibernating Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture)

(2010) Ada Yonath   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

From the Structure and Function of the Ribosome to New Antibiotics (Nobel Lecture)

(2010) Thomas A. Steitz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

Multiple pathways in the integration of proteins into the mitochondrial outer membrane

(2010) Jovana Dukanovic et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Chemo-Mechanical Coupling in F1-ATPase Revealed by Catalytic Site Occupancy during Catalysis

(2010) Rieko Shimo-Kon et al.   BIOPHYSICAL JOURNAL

Active Participation of the Mg2+Ion in the Reaction Coordinate of RNA Self-Cleavage Catalyzed by the Hammerhead Ribozyme

(2010) Kin-Yiu Wong et al.   Journal of Chemical Theory and Computation

What Makes Ras an Efficient Molecular Switch: A Computational, Biophysical, and Structural Study of Ras-GDP Interactions with Mutants of Raf

(2010) Daniel Filchtinski et al.   JOURNAL OF MOLECULAR BIOLOGY

Theoretical Study of Phosphodiester Hydrolysis in Nucleotide Pyrophosphatase/Phosphodiesterase. Environmental Effects on the Reaction Mechanism

(2010) Violeta López-Canut et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

(2010) S. C. L. Kamerlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes

(2010) Anna Rychkova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

(2010) B. van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mechanism for Activation of GTP Hydrolysis on the Ribosome

(2010) R. M. Voorhees et al.   SCIENCE

Protein kinases: evolution of dynamic regulatory proteins

(2010) Susan S. Taylor et al.   TRENDS IN BIOCHEMICAL SCIENCES

Efficient Catalytic Promiscuity for Chemically Distinct Reactions

(2009) Ann C. Babtie et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases

(2009) Shina C. L. Kamerlin et al.   BIOCHEMISTRY

Toward Accurate Screening in Computer-Aided Enzyme Design†

(2009) Maite Roca et al.   BIOCHEMISTRY

Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models

(2009) Shina C. L. Kamerlin et al.   CHEMPHYSCHEM

Drug Discovery and Protein Tyrosine Phosphatases

(2009) Mark Blaskovich   CURRENT MEDICINAL CHEMISTRY

Recent mechanistic insights into eukaryotic ribosomes

(2009) Marina V Rodnina et al.   CURRENT OPINION IN CELL BIOLOGY

GTPase activation of elongation factor EF-Tu by the ribosome during decoding

(2009) Jan-Christian Schuette et al.   EMBO JOURNAL

Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer

(2009) Abdulfattah Alkherraz et al.   FARADAY DISCUSSIONS

Did nature also choose arsenic?

(2009) Felisa Wolfe-Simon et al.   International Journal of Astrobiology

On the Energetics of ATP Hydrolysis in Solution

(2009) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phosphate Monoester Hydrolysis in Cyclohexane

(2009) Randy B. Stockbridge et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kinetic Analysis of β-Phosphoglucomutase and Its Inhibition by Magnesium Fluoride

(2009) Marko Goličnik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism and Transition State Structure of Aryl Methylphosphonate Esters Doubly Coordinated to a Dinuclear Cobalt(III) Center

(2009) Guoqiang Feng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

What recent ribosome structures have revealed about the mechanism of translation

(2009) T. Martin Schmeing et al.   NATURE

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

(2009) J. P. Schwans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases

(2009) H. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzyme millisecond conformational dynamics do not catalyze the chemical step

(2009) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

(2009) E. Villa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

(2009) Benjamin M. Messer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mapping catalytic promiscuity in the alkaline phosphatase superfamily

(2009) Stefanie Jonas et al.   PURE AND APPLIED CHEMISTRY

Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu

(2009) Xabier Agirrezabala et al.   QUARTERLY REVIEWS OF BIOPHYSICS

The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA

(2009) T. M. Schmeing et al.   SCIENCE

How Translocons Select Transmembrane Helices

(2008) Stephen H. White et al.   Annual Review of Biophysics

What we have learned from ribosome structures

(2008) V. Ramakrishnan   BIOCHEMICAL SOCIETY TRANSACTIONS

Promiscuous Sulfatase Activity and Thio-Effects in a Phosphodiesterase of the Alkaline Phosphatase Superfamily†

(2008) Jonathan K. Lassila et al.   BIOCHEMISTRY

Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor†

(2008) Demian Riccardi et al.   BIOCHEMISTRY

On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution†

(2008) Edina Rosta et al.   BIOCHEMISTRY

The energetics of the primary proton transfer in bacteriorhodopsin revisited: It is a sequential light-induced charge separation after all

(2008) Sonja Braun-Sand et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu

(2008) B.L. Grigorenko et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies

(2008) Shina C. L. Kamerlin et al.   CHEMPHYSCHEM

The Rap–RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues

(2008) Andrea Scrima et al.   EMBO JOURNAL

Role of Induced Fit in Enzyme Specificity: A Molecular Forward/Reverse Switch

(2008) Kenneth A. Johnson   JOURNAL OF BIOLOGICAL CHEMISTRY

A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum

(2008) Stefanie Jonas et al.   JOURNAL OF MOLECULAR BIOLOGY

Dineopentyl Phosphate Hydrolysis: Evidence for Stepwise Water Attack

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF ORGANIC CHEMISTRY

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Mechanics/Molecular Mechanics Investigation of the Chemical Reaction in Dpo4 Reveals Water-Dependent Pathways and Requirements for Active Site Reorganization

(2008) Yanli Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient Catalytic Promiscuity in an Enzyme Superfamily: An Arylsulfatase Shows a Rate Acceleration of 1013for Phosphate Monoester Hydrolysis

(2008) Luis F. Olguin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

(2008) Paul A. Sigala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase  

(2008) P. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation

(2008) D. Okuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How subunit coupling produces the  -subunit rotary motion in F1-ATPase

(2008) J. Pu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit

(2008) L. Lancaster et al.   RNA

Axle-Less F1-ATPase Rotates in the Correct Direction

(2008) Shou Furuike et al.   SCIENCE

DNA Polymerase β Fidelity:  Halomethylene-Modified Leaving Groups in Pre-Steady-State Kinetic Analysis Reveal Differences at the Chemical Transition State†

(2007) Christopher A. Sucato et al.   BIOCHEMISTRY