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Identification of hot regions in protein-protein interactions by sequential pattern mining.
(2007) BMC Bioinformatics 8 Suppl 5
PubMed: 17570867 | PubMedCentral: PMC1892096 | DOI: 10.1186/1471-2105-8-S5-S8
Table 1 Summary of the first dataset Query protein (Swiss-Prot AC number) Protein name PDB complex (PDB entry : chain) P09372 Protein grpE 1dkg :A P48052 Carboxypeptidase A2 precursor 1dtd :A P20936 R... s GTPase-activating protein 1 1wql :G P10824 Guanine nucleotide-binding protein G(i) 1agr :A P15153 Ras-related C3 botulinum toxin substrate 2 1ds6 :A Table 2 Summary of the second dataset, the protein-protein docking benchmark 2.0 Complex category Number of complexes Number of chains Enzyme-Inhibitor/Substrate 23 51 Antigen-bound Antibody 12 35 Antibody-Antigen 10 30 Others 39 104 Total in the dataset 72 220 Table 3 Comparing the efficiency of MAGIIC-PRO and ConSurf Query protein (PDB Code:Chain ID) MAGIIC-PRO (seconds) ConSurf (seconds) P09372 ( 1dkg :A) 10 590 P48052 ( 1dtd :A) 15 191 P20936 ( 1wql :G) 69 122 P10824 ( 1agr :A) 16 472 P15153 ( 1ds6 :A) 7 303 Table 4 Summary of the experimental results for the second dataset Number of tested protein chains 218 Number of patterns examined 212 Number of discovered blocks 900 Average number of blocks per protein chain 4.25 Average time used for each protein chain 11.76 seconds Number of blocks that is near interface 592 (~66%) Number of blocks that form clusters 832 (~92%) The maximum support of the patterns 100% The minimum support of the patterns 13% Average support of the patterns 66% Table 5 Clustering and interface propensities of the patterns derived for different categories of the proteins in the second dataset Complex Category Average clustering propensity Average interface propensity Original Non-redundant Original Non-redundant Enzyme-Inhibitor/Substrate 90.24% 87.54 79.24% 74.46 Antigen-bound Antibody 96.11% 93.69 66.31% 64.05 Antibody-Antigen 95.56% 92.22 57.72% 50.00 Others 92.05% 90.16 67.58% 65.53 Total average in the dataset 92.77% 89.98 68.63% 66.28 Table 6 The statistics on the block numbers of the derived patterns for 218 protein chains of the second dataset.
Pac Symp Biocomput 1998 401 412 9697199 Aloy P Querol E Aviles FX Sternberg MJ Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking J Mol Biol 2001 311 395 408 11478868 10.1006/jmbi.2001.4870 Res I Mihalek I Lichtarge O An evolution based classifier for prediction of protein interfaces without using protein structures Bioinformatics 2005 21 2496 2501 15728113 10.1093/bioinformatics/bti340 Ofran Y Rost B Predicted protein-protein interaction sites from local sequence information FEBS Lett 2003 544 236 239 12782323 10.1016/S0014-5793(03)00456-3 Yan C A two-stage classifier for identification of protein-protein interface residues Bioinformatics 2004 20 i371 i378 15262822 10.1093/bioinformatics/bth920 Madabushi S Yao H Marsh M Kristensen DM Philippi A Sowa ME Lichtarge O Structural clusters of evolutionary trace residues are statistically significant and common in proteins J Mol Biol 2002 316 139 154 11829509 10.1006/jmbi.2001.5327 Gallet X Charloteaux B Thomas A Brasseur R A fast method to predict protein interaction sites from sequences J Mol Biol 2000 302 917 926 10993732 10.1006/jmbi.2000.4092 Pei J Han J Mortazavi-Asl B Wang J Pinto H Chen Q Dayal U Hsu MC Mining sequential patterns by pattern-growth: the PrefixSpan approach IEEE Transactions on Knowledge and Data Engineering 2004 16 1424 1440 10.1109/TKDE.2004.77 Hsu CM Chen CY Hsu CC Liu BJ Carbonell JG, Siekmann J Efficient discovery of structural motifs from protein sequences with combination of flexible intra- and inter-block gap constraints Proceedings of the 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining: 9–12 April 2006; Sigapore 2006 LNCS 3918 Springer Berlin/Heidelberg 530 539 Rigoutsos I Floratos A Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm Bioinformatics 1998 14 55 67 9520502 10.1093/bioinformatics/14.1.55 Jonassen I Efficient discovery of conserved patterns using a pattern graph Comput Appl Biosci 1997 13 509 522 9367124 Califano A SPLASH: structural pattern localization analysis by sequential histograms Bioinformatics 2000 16 341 347 10869032 10.1093/bioinformatics/16.4.341 Gregory AP Dagmar R Gregory AP, Dagmar R Protein motifs Protein structure and function 2003 4 Waltham, MA: New Science Press Landgraf R Xenarios I Eisenberg D Three-dimensional cluster analysis identifies interfaces and functional residue clusters in protein J Mol Biol 2001 307 1487 1502 11292355 10.1006/jmbi.2001.4540 Berman HM The Protein Data Bank Nucleic Acids Res 2000 28 235 242 10592235 10.1093/nar/28.1.235 Mintseris J Wiehe K Pierce B Anderson R Chen R Janin J Weng Z Protein-Protein Docking Benchmark 2.0: an update Proteins 2005 60 214 216 15981264 10.1002/prot.20560 Li W Godzik A CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 2006 22 1658 1659 16731699 10.1093/bioinformatics/btl158 Online supplement of this paper Schueler-Furman O Baker D Conserved residue clustering and protein structure prediction Proteins 2003 52 225 235 12833546 10.1002/prot.10365 Ogiwara A Uchiyama I Yasuhiko S Kanehisa M Construction of dictionary of sequence motifs that characterize groups of related proteins Protein Eng 1992 5 479 488 1438158 10.1093/protein/5.6.479 Chakrabarti S Anand AP Bhardwaj N Pugalenthi G Sowdhamini R SCANMOT: searching for similar sequences using s simultaneous scan of multiple sequence motifs Nucleic Acids Res 2005 W274 W276 15980468 10.1093/nar/gki493 Hsu CM Chen CY Liu BJ WildSpan: efficient discovery of functional motifs spanning large wildcard regions from protein sequences Technical Report Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 1997 25 3389 3402 9254694 10.1093/nar/25.17.3389 Bairoch A Apweiler R Wu CH Barker WC Boeckmann B Ferro S Gasteiger E Huang H Lopez R Magrane M Martin MJ Natale DA O'Donovan C Redaschi N Yeh LS The universal protein resource (UniProt) Nucl Acids Res 2005 D154 D159 15608167 Pei J Han J Wang W Mining sequential patterns with constraints in large database Proceedings of the 11th ACM International Conference on Information and Knowledge Management: 4–9 November 2002; McLean ACM Press 18 25 Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proceedings of the National Academy of Sciences of the United States of America 1992 89 10915 10919 1438297 10.1073/pnas.89.22.10915 BLAST Database Landau M Mayrose I Rosenberg Y Glaser F Martz E Pupko T Ben-Tal N ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information Nucleic Acids Res 2005 W299 W302 15980475 10.1093/nar/gki370 Figures and Tables Figure 1 Representation of the GrpE-DnaKATPase complex [PDB: 1dkg ] with the pattern found by MAGIIC-PRO for GrpE protein.
Publication Year: 2007
Hsp70 chaperones: cellular functions and molecular mechanism.
(2005) Cell Mol Life Sci 62
PubMed: 15770419 | PubMedCentral: PMC2773841 | DOI: 10.1007/s00018-004-4464-6
( b ) Compex of the ATPase domain of DnaK with a dimer of GrpE X-ray structure of the complex of the DnaK ATPase domain (blue) and the GrpE dimer (orange and yellow; PDB entry code 1DKG; [ 60 ]).
Publication Year: 2005
Crystal structures of the ATPase domains of four human Hsp70 isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B', and HSPA5/BiP/GRP78.
(2010) PLoS One 5
PubMed: 20072699 | PubMedCentral: PMC2803158 | DOI: 10.1371/journal.pone.0008625
Sequences shown are human HSPA1A (1HJO; gi:5123454); HSPA1L (3GDQ; gi:124256496); HSPA2 (3I33; gi:13676857); bovine Hsc70 (PDB entry 1YUW; gi:76253709), E.coli DnaK (1DKG; gi:16128008); HSPA5 (3IUC; g... :16507237); HSPA9 (no structure available; gi:24234688); and HSPA6 (3FE1; gi:34419635).
Publication Year: 2010
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs.
(2010) PLoS Comput Biol 6
PubMed: 20862304 | PubMedCentral: PMC2940730 | DOI: 10.1371/journal.pcbi.1000931
Structural data We retrieved from the Protein Data Bank (PDB)  structural data for HSP70 ATPase domains complexed with GrpE (PDB id: 1DKG  ), BAG-1 (PDB id: 1HX...  ), HspBP1 (PDB id: 1XQS  ), and Sse1 (Hsp110, PDB id: 3D2E  ), shown in Figure 1b–e .
Structural diagrams are generated with PDB entries (b) 1DKG (c) 1HX1 (d) 3D2E (e) 1XQS.
An interdomain sector mediating allostery in Hsp70 molecular chaperones.
(2010) Mol Syst Biol 6
PubMed: 20865007 | PubMedCentral: PMC2964120 | DOI: 10.1038/msb.2010.65
( A ) In the ADP-bound state, nucleotide-binding and substrate-binding domains tumble independently of one another, the hydrophobic interdomain linker is relatively exposed, the β-sandwich sub... domain is relatively ordered, the lid sub-domain is closed, and substrate binds with high affinity (PDB codes 1DKG and 1DKZ).
Extent of structural asymmetry in homodimeric proteins: prevalence and relevance.
(2012) PLoS One 7
PubMed: 22629324 | PubMedCentral: PMC3358323 | DOI: 10.1371/journal.pone.0036688
The figure shows the structure of the 2∶1 complex of GrpE with DnaK (PDB: 1dkg).
Publication Year: 2012
Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK.
(2013) PLoS Comput Biol 9
PubMed: 24277995 | PubMedCentral: PMC3836694 | DOI: 10.1371/journal.pcbi.1003279
For example, a comparison of the crystal structures of the NBD in the apo form (1DKG)  and the ADP-bound form (1BUP  and 1KAZ  ) suggests a substantial, nucleotide-dependent movement in su... domain II-B ( Figure 1A ).
The structure 1DKG was crystallized without bound cofactors, so the essential ions, ATP, and ADP/P i were introduced by transferring the coordinates from the crystal structures of the closely related homolog, bovine Hsc70.
(A) Light grey cartoon represents Hsc70's NBD (PDB: 1BUP) in the “closed” conformation and the green cartoon is DnaK's NBD (PDB: 1DKG) in the “open” conformation.
Materials and Methods Molecular Dynamics Simulations Coordinates of E. coli DnaK NBD in complex with the nucleotide-exchange factor, GrpE (PDB: 1DKG  ) were obtained from the PDB, and GrpE was discarded.
Results/Discussion Dynamics Simulations of DnaK's NBD To initiate these studies, models of DnaK in different nucleotide states (apo, ATP-, and ADP/P i -bound) were constructed based on the crystal structure of the apo DnaK NBD (PDB: 1DKG).
Since 1DKG does not carry nucleotide and metal ions, these cofactors were introduced from structures of bovine Hsc70 (PDB: 1BUP and 1KAZ).
Publication Year: 2013
Molecular chaperones are nanomachines that catalytically unfold misfolded and alternatively folded proteins.
(2014) Cell Mol Life Sci 71
PubMed: 24760129 | PubMedCentral: PMC4131146 | DOI: 10.1007/s00018-014-1627-y
The misfolded conformers may then become a substrate of Hsp70 (PDB:1KHO) system (Hsp70–Hsp40 and nucleotide exchange factor, PDB:1DKG), which by reiterative cycles of binding, ATP-fueled unfol... ing and spontaneous refolding, converts the misfolded polypeptide into a native protein (cycle I).
Publication Year: 2014
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