Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching.

PubWeight™: 1.75‹?› | Rank: Top 3%

🔗 View Article (PMID 8953647)

Published in Proteins on November 01, 1996

Authors

P D Adams1, D M Engelman, A T Brünger

Author Affiliations

1: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

Articles citing this

An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91

TOXCAT: a measure of transmembrane helix association in a biological membrane. Proc Natl Acad Sci U S A (1999) 2.76

Role of receptor tyrosine kinase transmembrane domains in cell signaling and human pathologies. Biochemistry (2006) 1.96

FGFR3 dimer stabilization due to a single amino acid pathogenic mutation. J Mol Biol (2005) 1.59

An activating mutation in the CSF3R gene induces a hereditary chronic neutrophilia. J Exp Med (2009) 1.58

Amyloidogenic processing but not amyloid precursor protein (APP) intracellular C-terminal domain production requires a precisely oriented APP dimer assembled by transmembrane GXXXG motifs. J Biol Chem (2008) 1.54

How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci (2003) 1.38

Implications of threonine hydrogen bonding in the glycophorin A transmembrane helix dimer. Biophys J (2002) 1.34

Activation of Neu (ErbB-2) mediated by disulfide bond-induced dimerization reveals a receptor tyrosine kinase dimer interface. Mol Cell Biol (1998) 1.30

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23

Structure of the lethal phage pinhole. Proc Natl Acad Sci U S A (2009) 1.23

Interaction and conformational dynamics of membrane-spanning protein helices. Protein Sci (2009) 1.19

Roles of hydrophobicity and charge distribution of cationic antimicrobial peptides in peptide-membrane interactions. J Biol Chem (2012) 1.14

A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation. Biophys J (1999) 1.12

Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Sci (2002) 1.10

Mapping the energy surface of transmembrane helix-helix interactions. Biophys J (2001) 1.03

Lipid-modulated sequence-specific association of glycophorin A in membranes. Biophys J (2010) 1.01

Ab initio molecular-replacement phasing for symmetric helical membrane proteins. Acta Crystallogr D Biol Crystallogr (2007) 1.01

Multiple approaches converge on the structure of the integrin alphaIIb/beta3 transmembrane heterodimer. J Mol Biol (2009) 1.00

Thrombopoietin receptor activation: transmembrane helix dimerization, rotation, and allosteric modulation. FASEB J (2011) 1.00

Physical basis behind achondroplasia, the most common form of human dwarfism. J Biol Chem (2010) 0.99

Substitution rates in alpha-helical transmembrane proteins. Protein Sci (2001) 0.98

Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys J (2004) 0.98

Orientation-specific signalling by thrombopoietin receptor dimers. EMBO J (2011) 0.95

Activation of the erythropoietin receptor by the gp55-P viral envelope protein is determined by a single amino acid in its transmembrane domain. EMBO J (1999) 0.95

The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc (2013) 0.93

Molecular determinants and thermodynamics of the amyloid precursor protein transmembrane domain implicated in Alzheimer's disease. J Mol Biol (2011) 0.93

Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor. J Virol (2009) 0.93

Contribution of energy values to the analysis of global searching molecular dynamics simulations of transmembrane helical bundles. Biophys J (2002) 0.93

The assembly motif of a bacterial small multidrug resistance protein. J Biol Chem (2009) 0.91

Influence of the C-terminus of the glycophorin A transmembrane fragment on the dimerization process. Protein Sci (2000) 0.90

Helix packing and orientation in the transmembrane dimer of gp55-P of the spleen focus forming virus. Biophys J (2005) 0.87

Inside-out signaling promotes dynamic changes in the carcinoembryonic antigen-related cellular adhesion molecule 1 (CEACAM1) oligomeric state to control its cell adhesion properties. J Biol Chem (2013) 0.87

Molecular dynamics studies of the transmembrane domain of gp41 from HIV-1. Biochim Biophys Acta (2009) 0.87

Self-association of transmembrane domain 2 (TM2), but not TM1, in carnitine palmitoyltransferase 1A: role of GXXXG(A) motifs. J Biol Chem (2009) 0.87

Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adh Migr (2010) 0.85

Helix-bundle membrane protein fold templates. Protein Sci (1999) 0.85

Association of transmembrane helices: what determines assembling of a dimer? J Comput Aided Mol Des (2006) 0.83

Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain. J Virol (2013) 0.83

Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban. Biophys J (1998) 0.83

The dimeric transmembrane domain of prolyl dipeptidase DPP-IV contributes to its quaternary structure and enzymatic activities. Protein Sci (2010) 0.82

Structural and functional importance of transmembrane domain 3 (TM3) in the aspartate:alanine antiporter AspT: topology and function of the residues of TM3 and oligomerization of AspT. J Bacteriol (2009) 0.81

A structural model of EmrE, a multi-drug transporter from Escherichia coli. Biophys J (2004) 0.79

Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus. Biophys J (2003) 0.79

Molecular dynamics simulation approach for the prediction of transmembrane helix-helix heterodimers assembly. Eur Biophys J (2007) 0.79

Drugging Membrane Protein Interactions. Annu Rev Biomed Eng (2016) 0.78

Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. J Mol Model (2010) 0.78

Articles by these authors

Crystallographic R factor refinement by molecular dynamics. Science (1987) 15.90

Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem (1986) 11.00

The spontaneous insertion of proteins into and across membranes: the helical hairpin hypothesis. Cell (1981) 7.77

New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr D Biol Crystallogr (1996) 6.92

Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J Mol Biol (1983) 6.67

A transmembrane helix dimer: structure and implications. Science (1997) 6.46

The GxxxG motif: a framework for transmembrane helix-helix association. J Mol Biol (2000) 5.09

Membrane protein folding and oligomerization: the two-stage model. Biochemistry (1990) 4.86

Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. J Mol Biol (1994) 4.77

Path of the polypeptide in bacteriorhodopsin. Proc Natl Acad Sci U S A (1980) 4.76

Sequence specificity in the dimerization of transmembrane alpha-helices. Biochemistry (1992) 4.19

Bilayer structure in membranes. Nat New Biol (1971) 4.12

Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J Mol Biol (2000) 3.95

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc Natl Acad Sci U S A (1997) 3.64

Helical membrane protein folding, stability, and evolution. Annu Rev Biochem (2000) 3.63

Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices. J Biol Chem (1992) 3.52

Current models for the structure of biological membranes. J Cell Biol (1969) 3.47

Checking your imagination: applications of the free R value. Structure (1996) 3.40

Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution. Nat Struct Biol (1995) 3.36

X-ray diffraction studies of phase transitions in the membrane of Mycoplasma laidlawii. J Mol Biol (1970) 3.31

The effect of point mutations on the free energy of transmembrane alpha-helix dimerization. J Mol Biol (1997) 3.16

Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol (2000) 3.12

The Calpha ---H...O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci U S A (2001) 2.97

Structural changes are associated with soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor complex formation. J Biol Chem (1997) 2.96

Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins (1994) 2.94

A dimerization motif for transmembrane alpha-helices. Nat Struct Biol (1994) 2.82

Lipid bilayer structure in the membrane of Mycoplasma laidlawii. J Mol Biol (1971) 2.81

TOXCAT: a measure of transmembrane helix association in a biological membrane. Proc Natl Acad Sci U S A (1999) 2.76

Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng (1988) 2.74

Bacteriorhodopsin is an inside-out protein. Proc Natl Acad Sci U S A (1980) 2.72

Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science (1996) 2.65

The planar organization of lecithin-cholesterol bilayers. J Biol Chem (1972) 2.62

Refinement of the influenza virus hemagglutinin by simulated annealing. J Mol Biol (1990) 2.61

Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci U S A (2001) 2.47

A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science (1987) 2.43

Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J Magn Reson (1997) 2.31

Identification of a minimal core of the synaptic SNARE complex sufficient for reversible assembly and disassembly. Biochemistry (1998) 2.28

Refolding of bacteriorhodopsin in lipid bilayers. A thermodynamically controlled two-stage process. J Mol Biol (1987) 2.23

Phase improvement by cross-validated density modification. Acta Crystallogr D Biol Crystallogr (1995) 2.18

Two EGF molecules contribute additively to stabilization of the EGFR dimer. EMBO J (1997) 2.16

Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nat Struct Biol (1995) 2.15

Spontaneous, pH-dependent membrane insertion of a transbilayer alpha-helix. Biochemistry (1997) 2.11

Bacteriorhodopsin remains dispersed in fluid phospholipid bilayers over a wide range of bilayer thicknesses. J Mol Biol (1983) 2.07

Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP. Nat Struct Biol (1998) 2.05

The length of the flexible SNAREpin juxtamembrane region is a critical determinant of SNARE-dependent fusion. Mol Cell (1999) 1.99

Detergents modulate dimerization, but not helicity, of the glycophorin A transmembrane domain. J Mol Biol (1999) 1.94

Characterization of the plasma membrane of Mycoplasma laidlawii. I. Sodium dodecyl sulfate solubilization. Biochim Biophys Acta (1967) 1.90

Glycophorin A helical transmembrane domains dimerize in phospholipid bilayers: a resonance energy transfer study. Biochemistry (1994) 1.87

Characterization of the plasma membrane of Mycoplasma laidlawii. II. Modes of aggregation of solubilized membrane components. Biochim Biophys Acta (1967) 1.85

Molecular mechanism for the interaction of phospholipid with cholesterol. Nat New Biol (1972) 1.81

Specificity and promiscuity in membrane helix interactions. Q Rev Biophys (1994) 1.79

Specificity in transmembrane helix-helix interactions can define a hierarchy of stability for sequence variants. Proc Natl Acad Sci U S A (2001) 1.77

Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition. Nat Struct Biol (1998) 1.74

Truncated staphylococcal nuclease is compact but disordered. Proc Natl Acad Sci U S A (1992) 1.72

A structural change occurs upon binding of syntaxin to SNAP-25. J Biol Chem (1997) 1.72

Mutations can cause large changes in the conformation of a denatured protein. Biochemistry (1993) 1.69

Active site dynamics of ribonuclease. Proc Natl Acad Sci U S A (1985) 1.65

Surface area per lipid molecule in the intact membrane of the human red cell. Nature (1969) 1.65

Structural model of the phospholamban ion channel complex in phospholipid membranes. J Mol Biol (1995) 1.62

Analysis of a yeast SNARE complex reveals remarkable similarity to the neuronal SNARE complex and a novel function for the C terminus of the SNAP-25 homolog, Sec9. J Biol Chem (1997) 1.61

The glycophorin A transmembrane domain dimer: sequence-specific propensity for a right-handed supercoil of helices. Biochemistry (1992) 1.57

Structure-based prediction of the stability of transmembrane helix-helix interactions: the sequence dependence of glycophorin A dimerization. Proc Natl Acad Sci U S A (1998) 1.56

A neutron scattering study of the distribution of protein and RNA in the 30 S ribosomal subunit of Escherichia coli. J Mol Biol (1975) 1.54

Pair distribution functions of bacteriorhodopsin and rhodopsin in model bilayers. Biophys J (1983) 1.54

A zinc-binding domain involved in the dimerization of RAG1. J Mol Biol (1996) 1.53

Structural organization of the pentameric transmembrane alpha-helices of phospholamban, a cardiac ion channel. EMBO J (1994) 1.52

Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc Natl Acad Sci U S A (1986) 1.52

Dimerization of the p185neu transmembrane domain is necessary but not sufficient for transformation. Oncogene (1997) 1.52

The three-dimensional structure of alpha1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J (1986) 1.50

Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli. J Mol Biol (1988) 1.50

Inelastic neutron scattering analysis of hexokinase dynamics and its modification on binding of glucose. Nature (1982) 1.45

Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm. J Biomol NMR (1992) 1.43

Amphipols: polymeric surfactants for membrane biology research. Cell Mol Life Sci (2003) 1.42

Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study. Proc Natl Acad Sci U S A (1992) 1.40

Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J Mol Biol (2000) 1.35

A biophysical study of integral membrane protein folding. Biochemistry (1997) 1.35

Characterization of the plasma membrane of Mycoplasma laidlawii. IV. Structure and composition of membrane and aggregated components. Biochim Biophys Acta (1968) 1.33

Positions of proteins S6, S11 and S15 in the 30 S ribosomal subunit of Escherichia coli. J Mol Biol (1981) 1.31

Visual arrestin activity may be regulated by self-association. J Biol Chem (1999) 1.31

Yeast hexokinase in solution exhibits a large conformational change upon binding glucose or glucose 6-phosphate. Biochemistry (1979) 1.28

Calcium-induced increase in the radius of gyration and maximum dimension of calmodulin measured by small-angle X-ray scattering. Biochemistry (1985) 1.28

NMR analysis of helix I from the 5S RNA of Escherichia coli. Biochemistry (1992) 1.27

Are there dominant membrane protein families with a given number of helices? Proteins (1997) 1.26

Substrate binding closes the cleft between the domains of yeast phosphoglycerate kinase. J Biol Chem (1979) 1.24

Intramembrane helix-helix association in oligomerization and transmembrane signaling. Annu Rev Biophys Biomol Struct (1992) 1.24

Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin. J Mol Biol (1986) 1.24

Tertiary structure of bacteriorhodopsin. Positions and orientations of helices A and B in the structural map determined by neutron diffraction. J Mol Biol (1989) 1.24

Amino-acid substitutions in a surface turn modulate protein stability. Nat Struct Biol (1996) 1.22

Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2. J Mol Biol (1986) 1.22

Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H nuclear magnetic resonance and restrained molecular dynamics. J Mol Biol (1985) 1.21

Leucine side-chain rotamers in a glycophorin A transmembrane peptide as revealed by three-bond carbon-carbon couplings and 13C chemical shifts. J Biomol NMR (1996) 1.21

The direct rotation function: Patterson correlation search applied to molecular replacement. Acta Crystallogr D Biol Crystallogr (1995) 1.20

Microscopic theory of the dielectric properties of proteins. Biophys J (1991) 1.20

Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban. Biophys J (1996) 1.16