Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data.

Abstract:

:X-ray crystallography and NMR can provide detailed structural information of protein-protein complexes, but technical problems make their application challenging in the high-throughput regime. Other methods such as small-angle X-ray scattering (SAXS) are more promising for large-scale application, but at the cost of lower resolution, which is a problem that can be solved by complementing SAXS data with theoretical simulations. Here, we propose a novel strategy that combines SAXS data and accurate protein-protein docking simulations. The approach has been benchmarked on a large pool of known structures with synthetic SAXS data, and on three experimental examples. The combined approach (pyDockSAXS) provided a significantly better success rate (43% for the top 10 predictions) than either of the two methods alone. Further analysis of the influence of different docking parameters made it possible to increase the success rates for specific cases, and to define guidelines for improving the data-driven protein-protein docking protocols.

journal_name

J Mol Biol

authors

Pons C,D'Abramo M,Svergun DI,Orozco M,Bernadó P,Fernández-Recio J

doi

10.1016/j.jmb.2010.08.029

subject

Has Abstract

pub_date

2010-10-22 00:00:00

pages

217-30

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(10)00891-0

journal_volume

403

pub_type

杂志文章
  • The hypE gene completes the gene cluster for H2-oxidation in Azotobacter vinelandii.

    abstract::The nucleotide sequence was obtained for the hypE gene in the cluster of structural and accessory genes required for the assembly and functioning of the membrane-bound, dimeric, (NiFe)hydrogenase in Azotobacter vinelandii. The hypE gene encodes a polypeptide of 341 amino acid residues which is rich in alanine, glycine...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1149

    authors: Garg RP,Menon AL,Jacobs K,Robson RM,Robson RL

    更新日期:1994-02-11 00:00:00

  • Two slow stages in refolding of bovine carbonic anhydrase B are due to proline isomerization.

    abstract::Kinetics of refolding of bovine carbonic anhydrase B have been studied by the "double-jump" technique (i.e. the dependence of protein refolding on delay time in the unfolded state after fast unfolding). It is shown that two stages (the slow with a relaxation time of t1/2 approximately equal to 120 s and the superslow ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80215-3

    authors: Semisotnov GV,Uversky VN,Sokolovsky IV,Gutin AM,Razgulyaev OI,Rodionova NA

    更新日期:1990-06-05 00:00:00

  • Zooming in on Transcription Preinitiation.

    abstract::Class II gene transcription commences with the assembly of the Preinitiation Complex (PIC) from a plethora of proteins and protein assemblies in the nucleus, including the General Transcription Factors (GTFs), RNA polymerase II (RNA pol II), co-activators, co-repressors, and more. TFIID, a megadalton-sized multiprotei...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.04.003

    authors: Gupta K,Sari-Ak D,Haffke M,Trowitzsch S,Berger I

    更新日期:2016-06-19 00:00:00

  • Isolation, crystallization and preliminary diffraction analyses of human pancreatic alpha-amylase.

    abstract::Human pancreatic alpha-amylase has been isolated using a glycogen affinity precipitation procedure and crystallized in a form suitable for high resolution three-dimensional X-ray crystallographic analyses. Crystals are of the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 53.04 A, b = 74.80 A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1221

    authors: Burk D,Wang Y,Dombroski D,Berghuis AM,Evans SV,Luo Y,Withers SG,Brayer GD

    更新日期:1993-04-05 00:00:00

  • The ever changing moods of calmodulin: how structural plasticity entails transductional adaptability.

    abstract::The exceptional versatility of calmodulin (CaM) three-dimensional arrangement is reflected in the growing number of structural models of CaM/protein complexes currently available in the Protein Data Bank (PDB) database, revealing a great diversity of conformations, domain organization, and structural responses to Ca(2...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2014.05.016

    authors: Villarroel A,Taglialatela M,Bernardo-Seisdedos G,Alaimo A,Agirre J,Alberdi A,Gomis-Perez C,Soldovieri MV,Ambrosino P,Malo C,Areso P

    更新日期:2014-07-29 00:00:00

  • Defining the core structure of the alpha-lactalbumin molten globule state.

    abstract::Molten globules are partially folded states of proteins which are generally believed to mimic structures formed during the folding process. In order to determine the minimal requirements for the formation of a molten globule state, we have prepared a set of peptide models of the molten globule state of human alpha-lac...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3228

    authors: Demarest SJ,Boice JA,Fairman R,Raleigh DP

    更新日期:1999-11-19 00:00:00

  • Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots.

    abstract::The co-crystal structure of the MS2 coat protein dimer with its RNA operator reveals eight amino acid side-chains contacting seven of the RNA phosphates. These eight amino acids and five nearby control positions were individually changed to an alanine residue and the binding affinities of the mutant proteins to the RN...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.046

    authors: Hobson D,Uhlenbeck OC

    更新日期:2006-02-24 00:00:00

  • Segmental flexibility and head-head interaction in scallop myosin. A study using saturation transfer electron paramagnetic resonance spectroscopy.

    abstract::Saturation transfer electron paramagnetic resonance spectroscopy was used to investigate the rotational motion of the head domains of native and desensitized scallop myosin and its proteolytic subfragments. Scallop myosin was spin-labelled with 4-(2-iodoacetamido)-2,2,6,6-tetramethylpiperidinooxyl, which reacted with ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90090-6

    authors: Wells C,Bagshaw CR

    更新日期:1983-02-15 00:00:00

  • Increased thermostability and fidelity of DNA synthesis of wild-type and mutant HIV-1 group O reverse transcriptases.

    abstract::Reverse transcription coupled with DNA amplification has become a well-established and powerful molecular technique for studying ribonucleic acids. However, the efficiency of those reactions is largely dependent on the molecular properties of currently used reverse transcriptases (RTs). Engineered and natural RT varia...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.081

    authors: Alvarez M,Matamoros T,Menéndez-Arias L

    更新日期:2009-10-02 00:00:00

  • Mechanism of dissociative inhibition of HIV protease and its autoprocessing from a precursor.

    abstract::Dimerization is indispensible for release of the human immunodeficiency virus protease (PR) from its precursor (Gag-Pol) and ensuing mature-like catalytic activity that is crucial for virus maturation. We show that a single-chain Fv fragment (scFv) of a previously reported monoclonal antibody (mAb1696), which recogniz...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.05.024

    authors: Sayer JM,Aniana A,Louis JM

    更新日期:2012-09-14 00:00:00

  • Identification of an epitope in the C terminus of normal prion protein whose expression is modulated by binding events in the N terminus.

    abstract::We have characterized the epitopes of a panel of 12 monoclonal antibodies (Mabs) directed to normal human cellular prion protein (PrP(C)) using ELISA and Western blotting of recombinant PrP or synthetic peptide fragments of PrP. The first group of antibodies, which is represented by Mabs 5B2 and 8B4, reacts with PrP(2...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3986

    authors: Li R,Liu T,Wong BS,Pan T,Morillas M,Swietnicki W,O'Rourke K,Gambetti P,Surewicz WK,Sy MS

    更新日期:2000-08-18 00:00:00

  • Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?

    abstract::Grafting the antigen-binding loops onto a human antibody scaffold is a widely used technique to humanise murine antibodies. The success of this approach depends largely on the observation that the antigen-binding loops adopt only a limited number of canonical structures. Identification of the correct canonical structu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3839

    authors: Decanniere K,Muyldermans S,Wyns L

    更新日期:2000-06-30 00:00:00

  • Specific RNA-binding antibodies with a four-amino-acid code.

    abstract::Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.03.003

    authors: Sherman EM,Holmes S,Ye JD

    更新日期:2014-05-15 00:00:00

  • Comprehensive epitope analysis of monoclonal anti-proenkephalin antibodies using phage display libraries and synthetic peptides: revelation of antibody fine specificities caused by somatic mutations in the variable region genes.

    abstract::Filamentous phage libraries, displaying 6, 12 or 20 amino acid residue peptides at the N terminus of coat protein pIII were used to define and localize the epitopes of 15 monoclonal antibodies raised against human proenkephalin, a neuropeptide precursor. Eight monoclonal antibodies (PE14 to PE19, PE23 and PE25), which...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0191

    authors: Böttger V,Böttger A,Lane EB,Spruce BA

    更新日期:1995-04-14 00:00:00

  • Automatic definition of recurrent local structure motifs in proteins.

    abstract::An automatic procedure for defining recurrent folding motifs in proteins of known structure is described. These motifs are formed by short polypeptide fragments of equal size containing between four and seven residues. The method applies a classical clustering algorithm that operates on distances between selected back...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80194-9

    authors: Rooman MJ,Rodriguez J,Wodak SJ

    更新日期:1990-05-20 00:00:00

  • Interactions between morpholinyl anthracyclines and DNA. The crystal structure of a morpholino doxorubicin bound to d(CGTACG).

    abstract::Anthracycline antibiotics daunomycin and adriamycin are among the most widely used in cancer chemotherapy and DNA is believed to be the primary target of their biological action. The crystal structure of a morpholino derivative of adriamycin bound to the DNA hexamer d(CGTACG) has been determined at 1.5 A resolution. T...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1208

    authors: Cirilli M,Bachechi F,Ughetto G,Colonna FP,Capobianco ML

    更新日期:1993-04-05 00:00:00

  • The effect of regulatory Ca2+ on the in situ structures of troponin C and troponin I: a neutron scattering study.

    abstract::The effects of regulatory amounts of Ca2+ on the in situ structures of troponin C (TnC) and troponin I (TnI) in whole troponin have been investigated by neutron scattering. In separate difference experiments, 97% deuterated TnC and TnI within whole troponin were studied +/-Ca2+ in 41.6% 2H2O buffers in which protonate...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1965

    authors: Stone DB,Timmins PA,Schneider DK,Krylova I,Ramos CH,Reinach FC,Mendelson RA

    更新日期:1998-08-28 00:00:00

  • The C-Box Region of MAF1 Regulates Transcriptional Activity and Protein Stability.

    abstract::MAF1 is a conserved negative regulator of RNA polymerase (pol) III and intracellular lipid homeostasis across species. Here, we show that the MAF1 C-box region negatively regulates its activity. Mutations in Caenorhabditis elegans mafr-1 that truncate the C-box retain the ability to inhibit the transcription of RNA po...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.12.012

    authors: Pradhan A,Hammerquist AM,Khanna A,Curran SP

    更新日期:2017-01-20 00:00:00

  • Crystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti.

    abstract::A highly thermostable xylanase isolated from the thermophilic fungus Paecilomyces varioti has been crystallized by the vapour diffusion method. The isolation of this enzyme by crystallization directly from the culture filtrate projects this fungus as an important source for large-scale production of pure xylanase. The...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90052-3

    authors: Eswaramoorthy S,Vithayathil PJ,Viswamitra MA

    更新日期:1994-11-04 00:00:00

  • Domain structure and quaternary organization of the bacteriophage P22 Erf protein.

    abstract::The structure and activities of the recombination-promoting P22 Erf protein were examined in vitro. Treatment of the protein with elastase produces a stable amino-terminal fragment, consisting of amino acid residues 1 to (approximately) 136. We have purified this fragment, designated fragment B, to apparent homogeneit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90037-2

    authors: Poteete AR,Sauer RT,Hendrix RW

    更新日期:1983-12-25 00:00:00

  • Recapitulation of protein family divergence using flexible backbone protein design.

    abstract::We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.062

    authors: Saunders CT,Baker D

    更新日期:2005-02-18 00:00:00

  • Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism.

    abstract::The nature of the nucleation-collapse mechanism in protein folding is probed using 27-mer and 36-mer lattice models. Three different forms for the interaction potentials are used. Three of the four 27-mer sequences have maximally compact and identical native state while the other has a non-compact native conformation....

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1997

    authors: Klimov DK,Thirumalai D

    更新日期:1998-09-18 00:00:00

  • Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.

    abstract::The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II (TVAII) has been determined by multiple isomorphous replacement at 2.6 A resolution. TVAII was crystallized in an orthorhombic system with the space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5 A. There are two molecules i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2647

    authors: Kamitori S,Kondo S,Okuyama K,Yokota T,Shimura Y,Tonozuka T,Sakano Y

    更新日期:1999-04-16 00:00:00

  • Signal sequences containing multiple aromatic residues.

    abstract::Using homopolymeric units of either phenylalanine or tryptophan to replace the natural core segment of the Escherichia coli alkaline phosphatase signal peptide, the hydrophobicity requirements for protein export and processing were further explored. The mutant signal peptide containing polyphenylalanine functioned at ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90577-7

    authors: Rusch SL,Kendall DA

    更新日期:1992-03-05 00:00:00

  • Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola.

    abstract::The X-ray structures of two hemoglobins (Hb) from the sea cucumber Caudina arenicola (an echinoderm) have been determined: a low spin, hemichrome, monomeric Hb-C chain, and a cyanomet-liganded dimeric Hb-D chain. Attempts to obtain crystal structures of the deoxy-liganded and hemichrome forms from the same chain type ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0445

    authors: Mitchell DT,Kitto GB,Hackert ML

    更新日期:1995-08-18 00:00:00

  • The crystal structures of trout Hb I in the deoxy and carbonmonoxy forms.

    abstract::We have determined the X-ray crystallographic structure of trout Hb I in both the deoxy and carbonmonoxy forms to resolution limits of 2.3 angstroms and 2.5 angstroms, respectively. The overall fold of the molecule is highly similar to that of human HbA despite the low level of sequence identity between these proteins...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0355

    authors: Tame JR,Wilson JC,Weber RE

    更新日期:1996-06-21 00:00:00

  • Immunoaffinity enrichment coupled to quantitative mass spectrometry reveals ubiquitin-mediated signaling events.

    abstract::Ubiquitination is one of the most prevalent posttranslational modifications in eukaryotic cells, with functional importance in protein degradation, subcellular localization and signal transduction pathways. Immunoaffinity enrichment coupled with quantitative mass spectrometry enables the in-depth characterization of p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.03.018

    authors: Yu K,Phu L,Varfolomeev E,Bustos D,Vucic D,Kirkpatrick DS

    更新日期:2015-06-05 00:00:00

  • Structural basis for ASPP2 recognition by the tumor suppressor p73.

    abstract::Tumor suppressors p53, p63 and p73 comprise a family of stress-responsive transcription factors with distinct functions in development and tumor suppression. Most human cancers lose p53 function, yet all three proteins are capable of inducing apoptosis or cellular senescence. Mechanisms are therefore under investigati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.08.005

    authors: Canning P,von Delft F,Bullock AN

    更新日期:2012-11-02 00:00:00

  • Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.

    abstract::In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a long molecular dynamics trajectory of BPTI. Cross-relaxation rates were calculated from the trajectory by analysis of the appropriate proton-proton vector autocorrelation functions. A cr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2323

    authors: Schneider TR,Brünger AT,Nilges M

    更新日期:1999-01-15 00:00:00

  • Study of the active site residues of a glycoside hydrolase family 8 xylanase.

    abstract::Site-directed mutagenesis and a comparative characterisation of the kinetic parameters, pH dependency of activity and thermal stability of mutant and wild-type enzymes have been used in association with crystallographic analysis to delineate the functions of several active site residues in a novel glycoside hydrolase ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.09.064

    authors: Collins T,De Vos D,Hoyoux A,Savvides SN,Gerday C,Van Beeumen J,Feller G

    更新日期:2005-11-25 00:00:00