Published in Phys Chem Chem Phys on July 20, 2011
Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. J Phys Chem B (2013) 1.08
Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism. Biophys J (2013) 0.82
Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values. PLoS One (2012) 0.79
Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling. Proc Natl Acad Sci U S A (2015) 0.79
Effect of surfactant hydrophobicity on the pathway for unfolding of ubiquitin. J Am Chem Soc (2012) 0.77
The role of cross-chain ionic interactions for the stability of collagen model peptides. Biophys J (2013) 0.77
The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. J Mol Biol (2007) 2.35
Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes. Proc Natl Acad Sci U S A (2007) 1.98
Protein stability and surface electrostatics: a charged relationship. Biochemistry (2006) 1.70
Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. Nat Chem Biol (2006) 1.68
Cavities determine the pressure unfolding of proteins. Proc Natl Acad Sci U S A (2012) 1.52
The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation. Proc Natl Acad Sci U S A (2002) 1.47
Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. Proteins (2010) 1.45
Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci U S A (2009) 1.27
Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy. Biochemistry (2007) 1.24
Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. J Mol Biol (2010) 1.23
Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc Natl Acad Sci U S A (2005) 1.21
Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins (2005) 1.20
Enthalpy of helix-coil transition: missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues. Proc Natl Acad Sci U S A (2005) 1.11
Temperature dependence of the thermodynamics of helix-coil transition. J Mol Biol (2004) 1.10
Mechanism of fibril formation by a 39-residue peptide (PAPf39) from human prostatic acidic phosphatase. Biochemistry (2009) 1.09
Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. J Mol Biol (2002) 1.08
Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules. J Am Chem Soc (2014) 1.08
Removal of surface charge-charge interactions from ubiquitin leaves the protein folded and very stable. Protein Sci (2002) 1.06
Role of the charge-charge interactions in defining stability and halophilicity of the CspB proteins. J Mol Biol (2006) 1.02
Cell penetrating peptides: how do they do it? J Biol Phys (2008) 1.01
Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci (2007) 1.01
Size and sequence and the volume change of protein folding. J Am Chem Soc (2011) 1.00
Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin. Angew Chem Int Ed Engl (2005) 0.99
MHC-peptide binding is assisted by bound water molecules. J Mol Biol (2004) 0.98
Thermodynamics of the Trp-cage miniprotein unfolding in urea. Proteins (2010) 0.96
Structural basis for putrescine activation of human S-adenosylmethionine decarboxylase. Biochemistry (2008) 0.95
Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biol (2009) 0.94
Mirror images as naturally competing conformations in protein folding. J Phys Chem B (2012) 0.94
Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. J Phys Chem B (2012) 0.93
Core sequence of PAPf39 amyloid fibrils and mechanism of pH-dependent fibril formation: the role of monomer conformation. Biochemistry (2012) 0.92
An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface. Biophys J (2009) 0.91
Cooperativity of complex salt bridges. Protein Sci (2008) 0.91
How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin. Protein Eng Des Sel (2005) 0.90
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. J Mol Biol (2010) 0.89
Differential scanning calorimetry. Methods Mol Biol (2002) 0.89
Folding a protein in the computer: reality or hope? Structure (2005) 0.89
Conformational and thermodynamic properties of peptide binding to the human S100P protein. Protein Sci (2002) 0.89
Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy. J Am Chem Soc (2013) 0.89
Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer. Biochemistry (2005) 0.88
Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4. J Am Chem Soc (2006) 0.88
Folding of a highly conserved diverging turn motif from the SH3 domain. Biophys J (2003) 0.87
Statistical analysis of protein structures suggests that buried ionizable residues in proteins are hydrogen bonded or form salt bridges. Proteins (2011) 0.87
Annexin I and annexin II N-terminal peptides binding to S100 protein family members: specificity and thermodynamic characterization. Biochemistry (2009) 0.87
Isothermal titration calorimetry. Methods Mol Biol (2002) 0.87
The role and specificity of the catalytic and regulatory cation-binding sites of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae. J Biol Chem (2011) 0.87
Universal convergence of the specific volume changes of globular proteins upon unfolding. Biochemistry (2009) 0.87
Remodeling of the folding free energy landscape of staphylococcal nuclease by cavity-creating mutations. Biochemistry (2012) 0.86
A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. Methods Enzymol (2009) 0.86
The essential role of stacking adenines in a two-base-pair RNA kissing complex. J Am Chem Soc (2013) 0.86
The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. J Mol Biol (2010) 0.86
Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction. Proc Natl Acad Sci U S A (2012) 0.86
Protein conformational space populated in solution probed with aromatic residual dipolar (13) C-(1) H couplings. Chembiochem (2013) 0.86
Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain. Proteins (2011) 0.85
Structure-based design of a heptavalent anthrax toxin inhibitor. Biomacromolecules (2011) 0.85
Pressure perturbation calorimetry of unfolded proteins. J Phys Chem B (2010) 0.84
Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study. Proc Natl Acad Sci U S A (2010) 0.84
Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices. J Mol Biol (2002) 0.83
Enzyme activity in the crowded milieu. PLoS One (2012) 0.82
Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences. Biophys Chem (2006) 0.82
Modulation of quaternary structure of S100 proteins by calcium ions. Biophys Chem (2010) 0.82
Energetics of charge-charge interactions between residues adjacent in sequence. Proteins (2011) 0.82
Correction of apparent finite size effects in the area per lipid of lipid membranes simulations. J Chem Phys (2006) 0.82
Experimental test of the thermodynamic model of protein cooperativity using temperature-induced unfolding of a Ubq-UIM fusion protein. Biochemistry (2010) 0.81
Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement. J Am Chem Soc (2011) 0.81
NMR structure of the Apo-S100P protein. J Biomol NMR (2004) 0.80
Investigation of protein binding affinity in multimodal chromatographic systems using a homologous protein library. J Chromatogr A (2009) 0.80
Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values. PLoS One (2012) 0.79
Investigation of protein binding affinity and preferred orientations in ion exchange systems using a homologous protein library. Biotechnol Bioeng (2009) 0.79
Structural characterization of semen coagulum-derived SEM1(86-107) amyloid fibrils that enhance HIV-1 infection. Biochemistry (2014) 0.79
Bacterial expression and purification of the amyloidogenic peptide PAPf39 for multidimensional NMR spectroscopy. Protein Expr Purif (2013) 0.78
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins. Methods Enzymol (2009) 0.78
Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C. J Phys Chem B (2013) 0.78
Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity. Protein Sci (2003) 0.78
Equilibrium and kinetic studies of protein cooperativity using urea-induced folding/unfolding of a Ubq-UIM fusion protein. Biophys Chem (2011) 0.77
Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations. Proteins (2013) 0.77
Thermodynamic and kinetic analysis of peptides derived from CapZ, NDR, p53, HDM2, and HDM4 binding to human S100B. Biochemistry (2012) 0.77
The role of cross-chain ionic interactions for the stability of collagen model peptides. Biophys J (2013) 0.77
Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics. Biophys J (2008) 0.77
Novel interactions of the TRTK12 peptide with S100 protein family members: specificity and thermodynamic characterization. Biochemistry (2013) 0.77
Amino acid substitutions affecting protein dynamics in eglin C do not affect heat capacity change upon unfolding. Proteins (2006) 0.77
Molecular determinants of expansivity of native globular proteins: a pressure perturbation calorimetry study. J Phys Chem B (2014) 0.77
Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water. J Phys Chem B (2008) 0.76
Structural and thermodynamic characterization of the recognition of the S100-binding peptides TRTK12 and p53 by calmodulin. Protein Sci (2014) 0.75
Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding. J Phys Chem B (2017) 0.75
Both helical propensity and side-chain hydrophobicity at a partially exposed site in alpha-helix contribute to the thermodynamic stability of ubiquitin. Proteins (2005) 0.75
Advances in the analysis of conformational transitions in peptides using differential scanning calorimetry. Methods Mol Biol (2007) 0.75
Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge-Charge Interactions. J Phys Chem B (2015) 0.75
Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin. Phys Chem Chem Phys (2014) 0.75