当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Atomic environment energies in proteins defined from statistics of accessible and contact surface areas.

Atomic environment energies in proteins defined from statistics of accessible and contact surface areas.

Abstract：

:Atomic contact potentials are derived by statistical analysis of atomic surface contact areas versus atom type in a database of non-homologous protein structures. The atomic environment is characterized by the surface area accessible to solvent and the surface of contacts with polar and non-polar atoms. Four types of atoms are considered, namely neutral polar atoms from protein backbones and from protein side-chains, non-polar atoms and charged atoms. Potential energies delta Ej(E) are defined from the preference for an atom of type j to be in a given environment E compared to the expected value if everything was random; Boltzmann's law is then used to transform these preferences into energies. These new potentials very clearly discriminate misfolded from correct structural models. The performance of these potentials are critically assessed by monitoring the recognition of the native fold among a large number of alternative structural folding types (the hide-and-seek procedure), as well as by testing if the native sequence can be recovered from a large number of randomly shuffled sequences for a given 3D fold (a procedure similar to the inverse folding problem). We suggest that these potentials reflect the atomic short range non-local interactions in proteins. To characterise atomic solvation alone, similar potentials were derived as a function of the percentage of solvent-accessible area alone. These energies were found to agree reasonably well with the solvation formalism of Eisenberg and McLachlan.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Delarue M,Koehl P

doi

10.1006/jmbi.1995.0328

subject

Has Abstract

pub_date

1995-06-09 00:00:00

pages

675-90

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(85)70328-2

journal_volume

249

pub_type

杂志文章,评审

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Order-disorder phenomena in myelinated nerve sheaths: V. Effects of temperature on rat sciatic and optic nerves, and structural differences between the two types of nerve.

    abstract：:We describe in this work X-ray scattering and electron microscope studies of rat sciatic and optic nerves as a function of temperature. The scattering experiments were analyzed as described in the previous papers of this series: a variety of parameters were determined, some of which characterize the lattice disorder, ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.0011

    authors： Mateu L,Luzzati V,Vonasek E,Mateu E,Villegas GM,Vargas R

    更新日期：1995-01-13 00:00:00

  • Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA.

    abstract：:Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for C or G, / designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. Here, we show that BcnI functions as a monomer that interacts with its target DNA in 1:1 molar ratio and report cry...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.03.018

    authors： Sokolowska M,Kaus-Drobek M,Czapinska H,Tamulaitis G,Szczepanowski RH,Urbanke C,Siksnys V,Bochtler M

    更新日期：2007-06-08 00:00:00

  • Conserved patterns in the Cu,Zn superoxide dismutase family.

    abstract：:Conserved structural and functional features of Cu,Zn superoxide dismutase enzymes have been studied by comparison of known three-dimensional structures and analysis of the currently available amino acid sequences. For this purpose, the three-dimensional structures of the bovine, spinach and yeast enzymes have been su...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1298

    authors： Bordo D,Djinović K,Bolognesi M

    更新日期：1994-05-06 00:00:00

  • RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6.

    abstract：:phi 6 is an enveloped dsRNA bacterial virus. Its segmented genome resides inside the virion associated polymerase complex which is formed by four proteins (P1, P2, P4 and P7) encoded by the viral L segment. Complete and incomplete polymerase complex particles can be produced using cDNA copies of this largest genome se...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0317

    authors： Juuti JT,Bamford DH

    更新日期：1995-06-09 00:00:00

  • Isoform-selective interaction of the adaptor protein Tks5/FISH with Sos1 and dynamins.

    abstract：:The adaptor protein Tks5/FISH (tyrosine kinase substrate 5/five SH3 domains, hereafter termed Tks5) is a crucial component of a protein network that controls the invasiveness of cancer cells and progression of Alzheimer's disease. Tks5 consists of an amino-terminal PX domain that is followed by five SH3 domains (SH3A-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.05.025

    authors： Rufer AC,Rumpf J,von Holleben M,Beer S,Rittinger K,Groemping Y

    更新日期：2009-07-31 00:00:00

  • Consensus protein design without phylogenetic bias.

    abstract：:Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here, we show that randomization of a s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.04.039

    authors： Jäckel C,Bloom JD,Kast P,Arnold FH,Hilvert D

    更新日期：2010-06-18 00:00:00

  • Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis.

    abstract：:Dipicolinic acid (DPA) is a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance. Previous work has shown that mutations in the spoVF locus of Bacillus subtilis prevent the formation of DPA, a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1403

    authors： Daniel RA,Errington J

    更新日期：1993-07-20 00:00:00

  • Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.

    abstract：:Repeat proteins are formed from units of 20-40 aa that stack together into quasi one-dimensional non-globular structures. This modular repetitive construction means that, unlike globular proteins, a repeat protein's equilibrium folding and thus thermodynamic stability can be analysed using linear Ising models. Typical...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.02.022

    authors： Millership C,Phillips JJ,Main ER

    更新日期：2016-05-08 00:00:00

  • Occurrence of two architectural types of hexagonal bilayer hemoglobin in annelids: comparison of 3D reconstruction volumes of Arenicola marina and Lumbricus terrestris hemoglobins.

    abstract：:A 3D reconstruction at 25 A resolution of native hemoglobin of the polychaete worm Arenicola marina was carried out from frozen-hydrated specimens examined in the electron microscope. The reconstruction volume of this large extracellular multimeric respiratory pigment appears as a hexagonal bilayer structure with ecli...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4344

    authors： Jouan L,Taveau JC,Marco S,Lallier FH,Lamy JN

    更新日期：2001-01-26 00:00:00

  • Expression-system-dependent modulation of HIV-1 envelope glycoprotein antigenicity and immunogenicity.

    abstract：:Recombinant expression systems differ in the type of glycosylation they impart on expressed antigens such as the human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins, potentially affecting their biological properties. We performed head-to-head antigenic, immunogenic and molecular profiling of two distant...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.08.033

    authors： Kong L,Sheppard NC,Stewart-Jones GBE,Robson CL,Chen H,Xu X,Krashias G,Bonomelli C,Scanlan CN,Kwong PD,Jeffs SA,Jones IM,Sattentau QJ

    更新日期：2010-10-15 00:00:00

  • An unusual conformation of NAD+ bound to sorbitol dehydrogenase? A time-dependent transferred nuclear Overhauser effect study.

    abstract：:The conformation of NAD+ in the sheep liver sorbitol dehydrogenase-NAD+ binary complex has been investigated using time-dependent proton-proton transferred nuclear Overhauser enhancement measurements to determine interproton distance ratios and distances between bound NAD+ protons. The conformation about both the aden...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(84)80023-6

    authors： Gronenborn AM,Clore GM,Jeffery J

    更新日期：1984-02-05 00:00:00

  • The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation.

    abstract：:Enhanced structural insights into the folding energy landscape of the N-terminal dimerization domain of Escherichia coli tryptophan repressor, [2-66]2 TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined heli...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.07.080

    authors： Simler BR,Levy Y,Onuchic JN,Matthews CR

    更新日期：2006-10-13 00:00:00

  • Regulation of Mitochondrial Electron Transport Chain Assembly.

    abstract：:Mitochondrial function depends on the correct synthesis, transport, and assembly of proteins and cofactors of the electron transport chain. The initial idea that the respiratory chain protein complexes (RCCs) were independent structures in the inner mitochondrial membrane evolved after the identification of higher qua...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.09.016

    authors： Cogliati S,Lorenzi I,Rigoni G,Caicci F,Soriano ME

    更新日期：2018-12-07 00:00:00

  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry.

    abstract：:We have devised a molecular model building computer program (DEZYMER) which builds new ligand binding sites into a protein of known three-dimensional structure. It alters only the sequence and the side-chain structure of the protein, leaving the protein backbone fold intact by definition. The program searches for a co...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90510-d

    authors： Hellinga HW,Richards FM

    更新日期：1991-12-05 00:00:00

  • Monitoring sequence space as a test for the target of selection in viruses.

    abstract：:An essential feature of viral quasispecies, predicted from quasispecies theory, is that the target of selection is the mutant distribution as a whole. To test molecularly the mutant composition selected from a viral quasispecies we reconstructed a mutant distribution using 19 antigenic variants of foot-and-mouth disea...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.066

    authors： Perales C,Martín V,Ruiz-Jarabo CM,Domingo E

    更新日期：2005-01-21 00:00:00

  • Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft.

    abstract：:Penicillin G acylase is a periplasmic protein, cytoplasmically expressed as a precursor polypeptide comprising a signal sequence, the A and B chains of the mature enzyme (209 and 557 residues respectively) joined by a spacer peptide of 54 amino acid residues. The wild-type AB heterodimer is produced by proteolytic rem...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4105

    authors： Hewitt L,Kasche V,Lummer K,Lewis RJ,Murshudov GN,Verma CS,Dodson GG,Wilson KS

    更新日期：2000-09-29 00:00:00

  • Kinetic stability and crystal structure of the viral capsid protein SHP.

    abstract：:SHP, the capsid-stabilizing protein of lambdoid phage 21, is highly resistant against denaturant-induced unfolding. We demonstrate that this high functional stability of SHP is due to a high kinetic stability with a half-life for unfolding of 25 days at zero denaturant, while the thermodynamic stability is not unusual...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.09.030

    authors： Forrer P,Chang C,Ott D,Wlodawer A,Plückthun A

    更新日期：2004-11-12 00:00:00

  • The 29.9 kDa subunit of mitochondrial complex I is involved in the enzyme active/de-active transitions.

    abstract：:Mitochondrial respiratory chain complex I undergoes transitions from active to de-activated forms. We have investigated the phenomenon in sub-mitochondrial particles from Neurospora crassa wild-type and a null-mutant lacking the 29.9 kDa nuclear-coded subunit of complex I. Based on enzymatic activities, genetic crosse...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.06.005

    authors： Ushakova AV,Duarte M,Vinogradov AD,Videira A

    更新日期：2005-08-12 00:00:00

  • Fibrinogen structure in projection at 18 A resolution. Electron density by co-ordinated cryo-electron microscopy and X-ray crystallography.

    abstract：:Electron microscope images of frozen-hydrated crystals of a proteolytically modified fibrinogen show excellent preservation of the structure. An electron density map of the key centric projection of the crystal at 18 A resolution has been obtained by combining the phases derived from cryo-electron microscopy with X-ra...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90739-s

    authors： Rao SP,Poojary MD,Elliott BW Jr,Melanson LA,Oriel B,Cohen C

    更新日期：1991-11-05 00:00:00

  • Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3.

    abstract：:Based on sequence and phylogenetic analyses, glycoside hydrolase (GH) family 3 can be divided into several clusters that differ in the length of their primary sequences. However, structural data on representatives of GH3 are still scarce, since only three of their structures are known and only one of them has been tho...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.01.072

    authors： Pozzo T,Pasten JL,Karlsson EN,Logan DT

    更新日期：2010-04-02 00:00:00

  • Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions.

    abstract：:The sigma N class of sigma factors confer upon RNA polymerase the requirement for enhancer-binding activator proteins. The sigma-N (sigma N) protein of Klebsiella pneumoniae was analysed by the assay of purified peptides comprising domains or regions of sigma N defined by proteolysis or by homology alignment, respecti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0260

    authors： Cannon W,Missailidis S,Smith C,Cottier A,Austin S,Moore M,Buck M

    更新日期：1995-05-12 00:00:00

  • Eliminating the requirement of an essential gene product in an already very small virus: scaffolding protein B-free øX174, B-free.

    abstract：:Unlike most viral assembly systems, two scaffolding proteins, B and D, mediate bacteriophage øX174 morphogenesis. The external scaffolding protein D is highly ordered in the atomic structure and proper function is very sensitive to mutation. In contrast, the internal scaffolding protein B is relatively unordered and e...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.07.064

    authors： Chen M,Uchiyama A,Fane BA

    更新日期：2007-10-19 00:00:00

  • Thermal expansion of hen egg-white lysozyme. Comparison of the 1.9 A resolution structures of the tetragonal form of the enzyme at 100 K and 298 K.

    abstract：:The average structural and dynamic properties of tetragonal hen egg-white lysozyme have been compared, in structures refined at 1.9 A resolution, using data collected at 100 K and 298 K. The molecule expands by 1.8% over this temperature range with the expansion occurring primarily in its small sub-atomic-sized spaces...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80034-8

    authors： Young AC,Tilton RF,Dewan JC

    更新日期：1994-01-07 00:00:00

  • Spectroscopic studies on histone-DNA interactions. I. The interaction of histone (H2A, H2B) dimer with DNA: DNA sequence dependence.

    abstract：:Binding of the histone (H2A, H2B) dimer with chicken erythrocyte DNA has been studied by salt-titration spectroscopy in equilibrium conditions. The circular dichroism of DNA near 275 nm is depressed by the interaction with (H2A, H2B) at low concentrations of salt. The depression increases with increasing amounts of (H...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90699-1

    authors： Oohara I,Wada A

    更新日期：1987-07-20 00:00:00

  • Analysis of repeated motifs in the talin rod.

    abstract：:The amino acid sequence of the rod portion of talin contains strong periodic patterns with a long period of 32 to 34 residues superimposed on short periods of 7 and 7/2 residues. The rod includes 50 to 60 copies of an irregular repeated motif approximately 34 residues long. The motif itself consists of three sections:...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1081

    authors： McLachlan AD,Stewart M,Hynes RO,Rees DJ

    更新日期：1994-01-28 00:00:00

  • Facioscapulohumeral muscular dystrophy region gene 1 is a dynamic RNA-associated and actin-bundling protein.

    abstract：:FSHD region gene 1 (FRG1) is a dynamic nuclear and cytoplasmic protein that, in skeletal muscle, shows additional localization to the sarcomere. Maintaining appropriate levels of FRG1 protein is critical for muscular and vascular development in vertebrates; however, its precise molecular function is unknown. This stud...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.06.014

    authors： Sun CY,van Koningsbruggen S,Long SW,Straasheijm K,Klooster R,Jones TI,Bellini M,Levesque L,Brieher WM,van der Maarel SM,Jones PL

    更新日期：2011-08-12 00:00:00

  • Quality control in eukaryotic membrane protein overproduction.

    abstract：:The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a det...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.10.012

    authors： Thomas JA,Tate CG

    更新日期：2014-12-12 00:00:00

  • Crystallization and preliminary X-ray diffraction analysis of a type I beta-glucosidase encoded by the bgIA gene of Bacillus polymyxa.

    abstract：:The enzyme encoded by the bgIA gene of Bacillus polymyxa, a type I beta-glucosidase belonging to family I of glycosyl hydrolases, has been purified to homogeneity from an Escherichia coli culture which overexpressed the gene, and crystallized. The crystals, which diffract to 3.0 A resolution, belong to the orthorhombi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1441

    authors： Sanz-Aparicio J,Romero A,Martinez-Ripoll M,Madarro A,Flors A,Polaina J

    更新日期：1994-07-15 00:00:00

  • Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.

    abstract：:Proteins with ultra-fast folding/unfolding kinetics are excellent candidates for study by molecular dynamics. Here, we describe such simulations of a three helix bundle protein, the engrailed homeodomain (En-HD), which folds via the diffusion-collision model. The unfolding pathway of En-HD was characterized by seven s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.06.074

    authors： DeMarco ML,Alonso DO,Daggett V

    更新日期：2004-08-20 00:00:00

  • Oct-1 POU and octamer DNA co-operate to recognise the Bob-1 transcription co-activator via induced folding.

    abstract：:The expression of immunoglobulin genes is controlled in part by the DNA-binding protein Oct-1 and the B cell-specific transcription co-activator, Bob1 (also known as OCA-B or OBF-1) that together form a complex on the Igkappa promoter. We have characterised the assembly of the ternary complex using biophysical methods...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2711

    authors： Chang JF,Phillips K,Lundbäck T,Gstaiger M,Ladbury JE,Luisi B

    更新日期：1999-05-21 00:00:00