Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA.

PubWeight™: 1.46‹?› | Rank: Top 5%

🔗 View Article (PMC 283522)

Published in Proc Natl Acad Sci U S A on November 14, 2003

Authors

Michael F Hagan1, Aaron R Dinner, David Chandler, Arup K Chakraborty

Author Affiliations

1: Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA.

Articles citing this

CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71

Reaction coordinate of an enzymatic reaction revealed by transition path sampling. Proc Natl Acad Sci U S A (2007) 2.43

The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure (2010) 1.91

A mesoscale model of DNA and its renaturation. Biophys J (2009) 1.29

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc Natl Acad Sci U S A (2008) 1.21

Slow conformational motions that favor sub-picosecond motions important for catalysis. J Phys Chem B (2010) 1.13

A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. Biophys J (2005) 1.12

Activation mechanism of a signaling protein at atomic resolution from advanced computations. J Am Chem Soc (2007) 1.06

Kinetic pathways of beta-hairpin (un)folding in explicit solvent. Biophys J (2004) 1.05

Protein dynamics and enzymatic chemical barrier passage. J Phys Chem B (2011) 0.98

Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides. BMC Struct Biol (2007) 0.94

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS". J Chem Phys (2004) 0.92

Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations. Nucleic Acids Res (2011) 0.89

Base-flipping mechanism in postmismatch recognition by MutS. Biophys J (2011) 0.86

Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway. J Am Chem Soc (2012) 0.84

Protein dynamics and the enzymatic reaction coordinate. Top Curr Chem (2013) 0.83

Recent developments in methods for identifying reaction coordinates. Mol Simul (2014) 0.82

Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation. J Phys Chem B (2013) 0.80

Reducing the cost of evaluating the committor by a fitting procedure. J Chem Phys (2015) 0.80

Mapping L1 ligase ribozyme conformational switch. J Mol Biol (2012) 0.80

Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A (2015) 0.79

The effect of a G:T mispair on the dynamics of DNA. PLoS One (2013) 0.79

Folding kinetics for the conformational switch between alternative RNA structures. J Phys Chem B (2010) 0.78

Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study. J Chem Theory Comput (2013) 0.78

Close encounters with DNA. J Phys Condens Matter (2014) 0.77

Melting dynamics of short dsDNA chains in saline solutions. Springerplus (2015) 0.75

Articles cited by this

Kinetics of renaturation of DNA. J Mol Biol (1968) 25.41

Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci U S A (1987) 11.69

Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem (2001) 7.13

Translating biomolecular recognition into nanomechanics. Science (2000) 4.43

First-principles calculation of the folding free energy of a three-helix bundle protein. Science (1995) 4.19

DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol (1991) 3.93

A fluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles. Anal Chem (2000) 3.68

What controls the melting properties of DNA-linked gold nanoparticle assemblies? J Am Chem Soc (2003) 3.45

Statistical mechanics of a nonlinear model for DNA denaturation. Phys Rev Lett (1989) 2.90

Origin of nanomechanical cantilever motion generated from biomolecular interactions. Proc Natl Acad Sci U S A (2001) 2.22

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol (2002) 1.95

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A (2002) 1.78

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res (2003) 1.77

Transition-path sampling of beta-hairpin folding. Proc Natl Acad Sci U S A (2003) 1.61

Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides. Proc Natl Acad Sci U S A (1995) 1.19

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix. Chemphyschem (2001) 1.10

DNA dynamics in aqueous solution: opening the double helix. Int J Supercomput Appl (1990) 0.84

Melting of DNA oligomers: dynamical models and comparison with experimental results. J Biol Phys (1999) 0.81

Articles by these authors

Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem (2001) 7.13

Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys (2006) 6.51

Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell (2006) 5.39

The immunological synapse balances T cell receptor signaling and degradation. Science (2003) 4.94

T cell sensing of antigen dose governs interactive behavior with dendritic cells and sets a threshold for T cell activation. Nat Immunol (2008) 4.52

Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature (2010) 3.96

Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys. Nature (2013) 3.90

Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature (2010) 3.57

Digital signaling and hysteresis characterize ras activation in lymphoid cells. Cell (2009) 3.47

CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse. Nat Immunol (2004) 3.21

Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B (2005) 3.03

Drying-induced hydrophobic polymer collapse. Proc Natl Acad Sci U S A (2002) 2.56

Directed migration of positively selected thymocytes visualized in real time. PLoS Biol (2005) 2.46

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci U S A (2011) 2.37

Dynamic pathways for viral capsid assembly. Biophys J (2006) 2.23

The balance between T cell receptor signaling and degradation at the center of the immunological synapse is determined by antigen quality. Immunity (2008) 2.13

Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations. Biol Rev Camb Philos Soc (2011) 2.06

Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity (2013) 2.00

Telehealthcare for asthma. Cochrane Database Syst Rev (2010) 1.94

B cell antigen receptor signaling and internalization are mutually exclusive events. PLoS Biol (2006) 1.85

The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. PLoS Pathog (2013) 1.67

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain. Proc Natl Acad Sci U S A (2007) 1.67

Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nat Immunol (2011) 1.59

The impact of negative selection on thymocyte migration in the medulla. Nat Immunol (2009) 1.56

Understanding the structure and function of the immunological synapse. Cold Spring Harb Perspect Biol (2010) 1.54

Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4. Immunity (2013) 1.52

The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse. Immunity (2007) 1.52

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. J Chem Phys (2011) 1.47

Psychosis susceptibility gene ZNF804A and cognitive performance in schizophrenia. Arch Gen Psychiatry (2010) 1.46

Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE). Proc Natl Acad Sci U S A (2013) 1.44

Fast on-rates allow short dwell time ligands to activate T cells. Proc Natl Acad Sci U S A (2010) 1.43

Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same molecular signaling module. Proc Natl Acad Sci U S A (2007) 1.43

Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proc Natl Acad Sci U S A (2007) 1.42

Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. Proc Natl Acad Sci U S A (2008) 1.41

Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function. J Phys Chem B (2012) 1.40

The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A (2008) 1.39

The role of solvent fluctuations in hydrophobic assembly. J Phys Chem B (2008) 1.38

Contractile units in disordered actomyosin bundles arise from F-actin buckling. Phys Rev Lett (2012) 1.38

Dynamic order-disorder in atomistic models of structural glass formers. Science (2009) 1.37

Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys (2004) 1.36

Fluctuations of water near extended hydrophobic and hydrophilic surfaces. J Phys Chem B (2010) 1.36

Scaffold proteins confer diverse regulatory properties to protein kinase cascades. Proc Natl Acad Sci U S A (2007) 1.35

Instantaneous liquid interfaces. J Phys Chem B (2010) 1.35

How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc Natl Acad Sci U S A (2008) 1.32

Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies. J Gen Virol (2010) 1.30

CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery. Proc Natl Acad Sci U S A (2010) 1.28

Hybridization dynamics of surface immobilized DNA. J Chem Phys (2004) 1.27

Geometrical explanation and scaling of dynamical heterogeneities in glass forming systems. Phys Rev Lett (2002) 1.25

Corresponding states of structural glass formers. J Phys Chem B (2009) 1.25

Correlation of a dynamic model for immunological synapse formation with effector functions: two pathways to synapse formation. Trends Immunol (2002) 1.24

Efficient stochastic simulation of reaction-diffusion processes via direct compilation. Bioinformatics (2009) 1.23

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc Natl Acad Sci U S A (2008) 1.21

How antigen quantity and quality determine T-cell decisions in lymphoid tissue. Mol Cell Biol (2008) 1.20

Umbrella sampling for nonequilibrium processes. J Chem Phys (2007) 1.20

A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. Nat Immunol (2012) 1.18

Coarse-grained microscopic model of glass formers. Proc Natl Acad Sci U S A (2003) 1.18

The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II. J Chem Phys (2013) 1.17

An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Mol Syst Biol (2011) 1.17

Intracellular transport of insulin granules is a subordinated random walk. Proc Natl Acad Sci U S A (2013) 1.16

Deleterious GRM1 mutations in schizophrenia. PLoS One (2012) 1.16

Molecular flexibility can influence the stimulatory ability of receptor-ligand interactions at cell-cell junctions. Proc Natl Acad Sci U S A (2006) 1.16

Empty class II major histocompatibility complex created by peptide photolysis establishes the role of DM in peptide association. J Biol Chem (2007) 1.16

Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme. EMBO J (2010) 1.16

A mutation in an alternative untranslated exon of hexokinase 1 associated with hereditary motor and sensory neuropathy -- Russe (HMSNR). Eur J Hum Genet (2009) 1.15

Nonequilibrium umbrella sampling in spaces of many order parameters. J Chem Phys (2009) 1.14

Model of a fluid at small and large length scales and the hydrophobic effect. Phys Rev E Stat Nonlin Soft Matter Phys (2001) 1.14

Extended surfaces modulate hydrophobic interactions of neighboring solutes. Proc Natl Acad Sci U S A (2011) 1.14

Excitation lines and the breakdown of Stokes-Einstein relations in supercooled liquids. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 1.14

Space-time thermodynamics of the glass transition. Proc Natl Acad Sci U S A (2005) 1.13

Requirements for contractility in disordered cytoskeletal bundles. New J Phys (2012) 1.12

Movies, measurement, and modeling: the three Ms of mechanistic immunology. J Exp Med (2005) 1.10

Elastic energy storage in beta-sheets with application to F1-ATPase. Eur Biophys J (2003) 1.10

Evolving concepts of specificity in immune reactions. Proc Natl Acad Sci U S A (2010) 1.09

Decreased diacylglycerol metabolism enhances ERK activation and augments CD8+ T cell functional responses. J Biol Chem (2010) 1.09

Highly variable neural involvement in sphingomyelinase-deficient Niemann-Pick disease caused by an ancestral Gypsy mutation. Brain (2007) 1.08

A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency. PLoS Comput Biol (2010) 1.08

Monte Carlo simulations of biomolecules: The MC module in CHARMM. J Comput Chem (2006) 1.08

Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins. PLoS Comput Biol (2008) 1.07

Epigenetic estimation of age in humpback whales. Mol Ecol Resour (2014) 1.06

Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Res (2012) 1.06

Telehealthcare for asthma: a Cochrane review. CMAJ (2011) 1.05

Signatures of combinatorial regulation in intrinsic biological noise. Proc Natl Acad Sci U S A (2008) 1.05

Heterogeneity and growing length scales in the dynamics of kinetically constrained lattice gases in two dimensions. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.04

Corresponding states for mesostructure and dynamics of supercooled water. Faraday Discuss (2013) 1.03

Ndrg1 in development and maintenance of the myelin sheath. Neurobiol Dis (2011) 1.03

Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development (2010) 1.02

Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics (2011) 1.02

An improved coarse-grained model of solvation and the hydrophobic effect. J Chem Phys (2011) 1.02

Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline. PLoS One (2013) 1.02

Delineation of folding pathways of a β-sheet miniprotein. J Phys Chem B (2011) 1.01

Phase segregation on different length scales in a model cell membrane system. J Phys Chem B (2005) 1.01

Thymic selection of T-cell receptors as an extreme value problem. Phys Rev Lett (2009) 1.00

The unbinding of ATP from F1-ATPase. Biophys J (2003) 1.00

Decoupling of exchange and persistence times in atomistic models of glass formers. J Chem Phys (2007) 0.99

Autosomal-recessive congenital cerebellar ataxia is caused by mutations in metabotropic glutamate receptor 1. Am J Hum Genet (2012) 0.98

Dysregulated RasGRP1 responds to cytokine receptor input in T cell leukemogenesis. Sci Signal (2013) 0.98

Fluctuation-dissipation ratios in the dynamics of self-assembly. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.96