Thermodynamic and kinetic analysis of peptides derived from CapZ, NDR, p53, HDM2, and HDM4 binding to human S100B.

PubWeight™: 0.77‹?›

🔗 View Article (PMC 3448795)

Published in Biochemistry on August 29, 2012

Authors

Lucas N Wafer1, Werner W Streicher, Scott A McCallum, George I Makhatadze

Author Affiliations

1: Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.

Articles cited by this

(truncated to the top 100)

Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal Biochem (1989) 11.99

p53 mutant mice that display early ageing-associated phenotypes. Nature (2002) 10.05

Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A (1958) 9.18

Protein identification and analysis tools in the ExPASy server. Methods Mol Biol (1999) 6.31

Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature (2007) 6.26

Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci (2007) 5.81

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci U S A (2000) 5.71

Diffusion-controlled macromolecular interactions. Annu Rev Biophys Biophys Chem (1985) 4.87

Energetics of protein structure. Adv Protein Chem (1995) 4.82

The S100 family of EF-hand calcium-binding proteins: functions and pathology. Trends Biochem Sci (1996) 4.63

A soluble protein characteristic of the nervous system. Biochem Biophys Res Commun (1965) 4.22

Intracellular and extracellular roles of S100 proteins. Microsc Res Tech (2003) 3.70

The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur J Biochem (1977) 3.48

Regulation of p53 function and stability by phosphorylation. Mol Cell Biol (1999) 3.24

NDR kinases regulate essential cell processes from yeast to humans. Nat Rev Mol Cell Biol (2006) 2.88

Thermostability and aliphatic index of globular proteins. J Biochem (1980) 2.80

Structure of the negative regulatory domain of p53 bound to S100B(betabeta). Nat Struct Biol (2000) 2.72

A review of the S100 proteins in cancer. Eur J Surg Oncol (2007) 2.64

Calcium-dependent and -independent interactions of the S100 protein family. Biochem J (2006) 2.62

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics (2008) 2.50

Localizing the NADP+ binding site on the MurB enzyme by NMR. Nat Struct Biol (1996) 2.38

Structure of the MDM2/MDMX RING domain heterodimer reveals dimerization is required for their ubiquitylation in trans. Cell Death Differ (2008) 2.36

Mdm4 and Mdm2 cooperate to inhibit p53 activity in proliferating and quiescent cells in vivo. Proc Natl Acad Sci U S A (2006) 2.20

Calmodulin's flexibility allows for promiscuity in its interactions with target proteins and peptides. Mol Biotechnol (2004) 2.14

Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol (2008) 2.04

Molecular mechanism of the interaction between MDM2 and p53. J Mol Biol (2002) 2.03

Binding of S100 proteins to RAGE: an update. Biochim Biophys Acta (2008) 2.00

Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci U S A (1994) 1.99

Ca2+/S100 regulation of giant protein kinases. Nature (1996) 1.86

p53 contains large unstructured regions in its native state. J Mol Biol (2002) 1.75

The crystal structure of a complex of p11 with the annexin II N-terminal peptide. Nat Struct Biol (1999) 1.72

Inflammation-associated S100 proteins: new mechanisms that regulate function. Amino Acids (2010) 1.65

Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J Mol Biol (2009) 1.62

Proteins of the S100 family regulate the oligomerization of p53 tumor suppressor. Proc Natl Acad Sci U S A (2005) 1.52

Energetics of target peptide binding by calmodulin reveals different modes of binding. J Biol Chem (2001) 1.44

Solution structure of calcium-bound rat S100B(betabeta) as determined by nuclear magnetic resonance spectroscopy,. Biochemistry (1998) 1.42

Antigen recognition by conformational selection. FEBS Lett (1999) 1.42

Structural basis of the Ca(2+)-dependent association between S100C (S100A11) and its target, the N-terminal part of annexin I. Structure (2000) 1.34

Genomic and functional profiling of human Down syndrome neural progenitors implicates S100B and aquaporin 4 in cell injury. Hum Mol Genet (2007) 1.33

Enzyme dynamics along the reaction coordinate: critical role of a conserved residue. Biochemistry (2006) 1.31

The amino-acid sequence of S-100 protein (PAP I-b protein) and its relation to the calcium-binding proteins. Eur J Biochem (1978) 1.31

Mechanism of Ca2+-mediated regulation of NDR protein kinase through autophosphorylation and phosphorylation by an upstream kinase. J Biol Chem (2002) 1.30

Structure of the Ca2+/S100B/NDR kinase peptide complex: insights into S100 target specificity and activation of the kinase. Biochemistry (2003) 1.30

The three-dimensional solution structure of Ca(2+)-bound S100A1 as determined by NMR spectroscopy. J Mol Biol (2005) 1.29

The Ca(2+)-dependent interaction of S100B(beta beta) with a peptide derived from p53. Biochemistry (1998) 1.28

Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. Proc Natl Acad Sci U S A (2011) 1.26

Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12. J Mol Biol (2002) 1.25

Characterization of S-100b binding epitopes. Identification of a novel target, the actin capping protein, CapZ. J Biol Chem (1995) 1.25

Modulation of the oligomerization state of p53 by differential binding of proteins of the S100 family to p53 monomers and tetramers. J Biol Chem (2009) 1.25

Dynamics and mechanisms of coupled protein folding and binding reactions. Curr Opin Struct Biol (2011) 1.25

Differential expression of S100 protein subtypes in malignant melanoma, and benign and malignant peripheral nerve sheath tumors. J Cutan Pathol (2008) 1.24

Recognition of the tumor suppressor protein p53 and other protein targets by the calcium-binding protein S100B. Biochim Biophys Acta (2006) 1.24

Deciphering rules of helix stability in peptides. Methods Enzymol (1998) 1.23

Quantitative analysis of multisite protein-ligand interactions by NMR: binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP. J Am Chem Soc (2012) 1.22

The structure of calcyclin reveals a novel homodimeric fold for S100 Ca(2+)-binding proteins. Nat Struct Biol (1995) 1.19

Immunohistochemical localization of S-100 protein in granular cell myoblastoma. Cancer (1982) 1.18

A novel calcium-sensitive switch revealed by the structure of human S100B in the calcium-bound form. Structure (1998) 1.15

Calcium-binding properties of wild-type and EF-hand mutants of S100B in the presence and absence of a peptide derived from the C-terminal negative regulatory domain of p53. Biochemistry (2005) 1.14

MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR (2003) 1.14

The solution structure of the bovine S100B protein dimer in the calcium-free state. Structure (1996) 1.12

Capillarity theory for the fly-casting mechanism. Proc Natl Acad Sci U S A (2010) 1.11

Kinetics of folding and binding of an intrinsically disordered protein: the inhibitor of yeast aspartic proteinase YPrA. J Am Chem Soc (2008) 1.09

What is the time scale for α-helix nucleation? J Am Chem Soc (2011) 1.09

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions. Proteins (2011) 1.08

A novel mode of target recognition suggested by the 2.0 A structure of holo S100B from bovine brain. Structure (1998) 1.07

Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding. Proc Natl Acad Sci U S A (2003) 1.06

Serum levels of S100B and NSE proteins in Alzheimer's disease patients. J Neuroinflammation (2010) 1.05

Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting". J Am Chem Soc (2009) 1.04

Members of the S100 family bind p53 in two distinct ways. Protein Sci (2008) 1.03

Both Ca2+ and Zn2+ are essential for S100A12 protein oligomerization and function. BMC Biochem (2009) 1.03

Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants. Proteins (2008) 1.02

The effects of CapZ peptide (TRTK-12) binding to S100B-Ca2+ as examined by NMR and X-ray crystallography. J Mol Biol (2010) 1.01

A novel S100 target conformation is revealed by the solution structure of the Ca2+-S100B-TRTK-12 complex. J Biol Chem (2002) 1.01

S100B(betabeta) inhibits the protein kinase C-dependent phosphorylation of a peptide derived from p53 in a Ca2+-dependent manner. Protein Sci (1998) 0.99

Solution structure of S100A1 bound to the CapZ peptide (TRTK12). J Mol Biol (2009) 0.97

Thermodynamics of the Trp-cage miniprotein unfolding in urea. Proteins (2010) 0.96

Molecular characterization and tissue distribution of a novel member of the S100 family of EF-hand proteins. Biochemistry (2001) 0.96

Direct assessment of the α-helix nucleation time. J Phys Chem B (2011) 0.95

Diffusion-controlled reactions of enzymes. A comparison between Chou's model and Alberty-Hammes-Eigen's model. Eur J Biochem (1982) 0.94

Role of the C-terminal extension in the interaction of S100A1 with GFAP, tubulin, the S100A1- and S100B-inhibitory peptide, TRTK-12, and a peptide derived from p53, and the S100A1 inhibitory effect on GFAP polymerization. Biochem Biophys Res Commun (1999) 0.94

Effects of S100A1 and S100B on microtubule stability. An in vitro study using triton-cytoskeletons from astrocyte and myoblast cell lines. Neuroscience (2000) 0.94

Crystal structure of the S100A4-nonmuscle myosin IIA tail fragment complex reveals an asymmetric target binding mechanism. Proc Natl Acad Sci U S A (2012) 0.93

Specificity and Zn2+ enhancement of the S100B binding epitope TRTK-12. J Biol Chem (1999) 0.93

Structural changes in the C-terminus of Ca2+-bound rat S100B (beta beta) upon binding to a peptide derived from the C-terminal regulatory domain of p53. Protein Sci (1999) 0.92

Oligomerization and divalent ion binding properties of the S100P protein: a Ca2+/Mg2+-switch model. J Mol Biol (1998) 0.91

Cloning, overexpression, purification, and spectroscopic characterization of human S100P. Protein Sci (1998) 0.90

Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase. Biochemistry (2000) 0.90

Transcriptional regulation and functional implication of S100P in cancer. Amino Acids (2010) 0.89

Conformational and thermodynamic properties of peptide binding to the human S100P protein. Protein Sci (2002) 0.89

The dimerization interface of the metastasis-associated protein S100A4 (Mts1): in vivo and in vitro studies. J Biol Chem (2001) 0.88

High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins. J Biomol NMR (1999) 0.88

Puzzling over MDM4-p53 network. Int J Biochem Cell Biol (2010) 0.88

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 S100B/RAGE Axis in Alzheimer's Disease. Cardiovasc Psychiatry Neurol (2010) 0.86

MDM4 binds ligands via a mechanism in which disordered regions become structured. FEBS Lett (2010) 0.85

S100 proteins interact with the N-terminal domain of MDM2. FEBS Lett (2010) 0.85

Design of high-affinity S100-target hybrid proteins. Protein Sci (2009) 0.85

Molecular basis of S100 proteins interacting with the p53 homologs p63 and p73. Oncogene (2010) 0.85

Diffusion-controlled reactions of enzymes. An approximate analytic solution of Chou's model. Biophys Chem (1983) 0.83

Articles by these authors

Structure of C3b in complex with CRIg gives insights into regulation of complement activation. Nature (2006) 2.69

The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. J Mol Biol (2007) 2.35

Solution structures of chemoenzymatically synthesized heparin and its precursors. J Am Chem Soc (2008) 2.02

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

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

NMR methods for studying the structure and dynamics of RNA. Chembiochem (2005) 1.36

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

Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex. Biochemistry (2003) 1.14

MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR (2003) 1.14

Comparison of the global structure and dynamics of native and unmodified tRNAval. Biochemistry (2005) 1.13

Highly conserved histidine plays a dual catalytic role in protein splicing: a pKa shift mechanism. J Am Chem Soc (2009) 1.12

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

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

Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci (2007) 1.01

Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin. Angew Chem Int Ed Engl (2005) 0.99

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

NMR investigation of the role of osteocalcin and osteopontin at the organic-inorganic interface in bone. Langmuir (2013) 0.93

Methyl dynamics of the amyloid-beta peptides Abeta40 and Abeta42. Biochem Biophys Res Commun (2007) 0.93

Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. J Phys Chem B (2012) 0.93

M35 oxidation induces Abeta40-like structural and dynamical changes in Abeta42. J Am Chem Soc (2008) 0.92

Core sequence of PAPf39 amyloid fibrils and mechanism of pH-dependent fibril formation: the role of monomer conformation. Biochemistry (2012) 0.92

Binding affinities of vascular endothelial growth factor (VEGF) for heparin-derived oligosaccharides. Biosci Rep (2012) 0.91

Cooperativity of complex salt bridges. Protein Sci (2008) 0.91

Domain structure elucidation of human decorin glycosaminoglycans. Biochem J (2010) 0.91

How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin. Protein Eng Des Sel (2005) 0.90

Differential scanning calorimetry. Methods Mol Biol (2002) 0.89

Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. J Mol Biol (2010) 0.89

Conformational and thermodynamic properties of peptide binding to the human S100P protein. Protein Sci (2002) 0.89

Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4. J Am Chem Soc (2006) 0.88

Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer. Biochemistry (2005) 0.88

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

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

Isothermal titration calorimetry. Methods Mol Biol (2002) 0.87

Universal convergence of the specific volume changes of globular proteins upon unfolding. Biochemistry (2009) 0.87

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

A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. Methods Enzymol (2009) 0.86

Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain. Proteins (2011) 0.85

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein. Phys Chem Chem Phys (2011) 0.84

Pressure perturbation calorimetry of unfolded proteins. J Phys Chem B (2010) 0.84

Identifying specific protein residues that guide surface interactions and orientation on silica nanoparticles. Langmuir (2013) 0.84

Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices. J Mol Biol (2002) 0.83

Modulation of quaternary structure of S100 proteins by calcium ions. Biophys Chem (2010) 0.82

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences. Biophys Chem (2006) 0.82

Energetics of charge-charge interactions between residues adjacent in sequence. Proteins (2011) 0.82

Enzyme activity in the crowded milieu. PLoS One (2012) 0.82

Nuclear magnetic resonance quantification for monitoring heparosan K5 capsular polysaccharide production. Anal Biochem (2009) 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

Investigation of protein binding affinity in multimodal chromatographic systems using a homologous protein library. J Chromatogr A (2009) 0.80

NMR structure of the Apo-S100P protein. J Biomol NMR (2004) 0.80

Structural characterization of semen coagulum-derived SEM1(86-107) amyloid fibrils that enhance HIV-1 infection. Biochemistry (2014) 0.79

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

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

Self-assembly of designed coiled coil peptides studied by small-angle X-ray scattering and analytical ultracentrifugation. J Pept Sci (2013) 0.78

Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins. Methods Enzymol (2009) 0.78

Synthesis and characterization of fluorescent displacers for online monitoring of displacement chromatography. J Am Chem Soc (2008) 0.78

Bacterial expression and purification of the amyloidogenic peptide PAPf39 for multidimensional NMR spectroscopy. Protein Expr Purif (2013) 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

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

The role of cross-chain ionic interactions for the stability of collagen model peptides. Biophys J (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

Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR. Proc Natl Acad Sci U S A (2010) 0.76

Investigation into the molecular and thermodynamic basis of protein interactions in multimodal chromatography using functionalized nanoparticles. Langmuir (2014) 0.76

High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States. J Am Chem Soc (2016) 0.76

Data requirements for reliable chemical shift assignments in deuterated proteins. J Biomol NMR (2003) 0.76

Structural and thermodynamic characterization of the recognition of the S100-binding peptides TRTK12 and p53 by calmodulin. Protein Sci (2014) 0.75

Effects of urea on selectivity and protein-ligand interactions in multimodal cation exchange chromatography. Langmuir (2012) 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

Mobile phase modifier effects in multimodal cation exchange chromatography. Biotechnol Bioeng (2011) 0.75

An affinity-based strategy for the design of selective displacers for the chromatographic separation of proteins. Langmuir (2008) 0.75

Advances in the analysis of conformational transitions in peptides using differential scanning calorimetry. Methods Mol Biol (2007) 0.75

Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding. J Phys Chem B (2017) 0.75

Mechanistic studies of displacer-protein binding in chemically selective displacement systems using NMR and MD simulations. Biotechnol Bioeng (2009) 0.75

1H, 13C, and 15N resonance assignments of SAP18. J Biomol NMR (2005) 0.75

Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge-Charge Interactions. J Phys Chem B (2015) 0.75

Probing multimodal ligand binding regions on ubiquitin using nuclear magnetic resonance, chromatography, and molecular dynamics simulations. J Chromatogr A (2012) 0.75