Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 19

Citations in PubMed

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PDB ID Mentions in PubMed Central

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In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.

(2007) BMC Struct Biol 7

PubMed: 17559675 | PubMedCentral: PMC1913526 | DOI: 10.1186/1472-6807-7-37

The C α -RMSD between isolated (PDB entry 1B1I, resolution 1.8 Å) [ 42 ] and hRI-bound Ang (PDB entry 1A4Y, resolution 2.0 Å) is 1.07 Å.

The segments named A and B in the 2.0 Å resolution structure corresponding to the PDB entry 1A4Y[ 11 ] were used to model the bound structures of hRI and Ang, respectively.

Publication Year: 2007


Multiple domain insertions and losses in the evolution of the Rab prenylation complex.

(2007) BMC Evol Biol 7

PubMed: 17705859 | PubMedCentral: PMC1994686 | DOI: 10.1186/1471-2148-7-140

Figure 3 Maximum Likelihood reconstruction of the evolutionary relationships between the LRR domains found in RGGTase a-subunit (red branches) and reference sequences representing other superfamilies ... f LRR domains – L-domain-like, internalin LRR ( 106v ) – green; RNI-like, 28-residue LRR, Ribonucelase inhibitor ( 1A4Y ) – blue; RNI-like, RanGAP1, N-terminal domain( 1K5D ) – purple; outer arm dynein light chain( 1M9L ) – orange; L-domain-like, RabGGTase α-subunit, C-terminal domain ( 1LTX ) – red.

Publication Year: 2007


The modular organization of domain structures: insights into protein-protein binding.

(2007) PLoS Comput Biol 3

PubMed: 18069884 | PubMedCentral: PMC2134966 | DOI: 10.1371/journal.pcbi.0030239

The modular division of the RI (PDB ID: 1a4y, chain D) clearly shows that the hotspot region and Trp-rich area are fully contained in two different modules ( Figure 6 F).

PDB ID: 1a4y, chain D. TEM1.

Publication Year: 2007


Spatial chemical conservation of hot spot interactions in protein-protein complexes.

(2007) BMC Biol 5

PubMed: 17925020 | PubMedCentral: PMC2231411 | DOI: 10.1186/1741-7007-5-43

Sens. 1a4y:A RNase inhibitor Angiogenin 4 0.74 0.78 0.75 0.18 0.78 0 0.75 0.8 14 1brs:A Barnase Barstar 6 0.75 1 0.5 n/a n/a n/a 0.5 0.67 8 1brs:D Barstar Barnase 6 1 1 1 n/a n/a n/a 1 1 6 1cbw I BPTI... Trypsin 7 1 0.88 1 0.75 0.62 1 0.75 1 9 1gc1:C CD4 gp120 6 0.74 0.86 0.67 0.58 0.62 0.67 0.81 0.33 49 1bxi:A Im9 E9 DNase 6 0.72 1 0.44 0.72 0.88 0.56 0.88 0.44 28 1dan:L Factor VII Tissue Factor 6 1 0.73 1 0.23 0.64 0 0.73 1 107 1jck:A TCR Vb SEC3 6 0.65 0.88 0.4 0.41 0.75 0 1 0.5 24 1jck:B SEC3 TCR Vb 6 0.75 1 0.5 0.31 0.5 0.12 1 0.62 10 1vfb:C HEL D.1.3 7 0.51 0.62 0.5 0.27 0.62 0.25 1 0 12 3hfm:Y HEL HYHEL 8 0.62 0.6 0.67 0.78 0.7 0.67 0.8 1 13 3hhr:A hGH hGHbp 4 0.74 1 0.52 0.59 0.44 0.68 0.94 0.32 161 Mean MAPPIS Mean Consurf Mean Robetta Total 6 0.77 0.86 0.66 0.48 0.66 0.4 0.85 0.64 440 (116) We compared the predictive power of MAPPIS with our previously developed multiple alignment methods.

Publication Year: 2007


Identification of hot-spot residues in protein-protein interactions by computational docking.

(2008) BMC Bioinformatics 9

PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447

Table 1 Initial dataset of complexes used in this work Complex a Res b Receptor Ligand Unbound receptor Res b Unbound ligand Res b Complex type c 1A22 2.60 Growth hormone receptor Growth hormone - - 1... GU 2.50 B/U 1A4Y 2.00 Ribonuclease inhibitor Angiogenin - - 1UN3 1.70 B/U 1AHW 3.00 Fab 5G9 Tissue Factor 1K6Q 2.40 2HFT 1.69 U/U 1AIE 1.50 p53 p53 - - - - B/B 1BRS 2.00 Barnase Barstar 1A2P 1.50 - - U/B 1BXI 2.05 Colicin E9 Immunity protein Im9 1FSJ 1.80 - - U/B 1DAN 2.00 Tissue Factor Factor VII 2HFT 1.69 - - U/B 1DFJ 2.30 Ribonuclease A Ribonuclease inhibitor 1FS3 1.40 2BNH 2.30 U/U 1DN2 2.70 IgG1 Fc fragment DCAWHLGELV WCT-NH 2 1H3V 3.10 - - U/B 3HFM 3.00 HYHEL-10 HEL 1GPO 1.95 3LZT 0.92 U/U 1GC1 2.50 CD4 gp120 1CDJ 2.50 - - U/B 1F47 1.95 Zipa FTSZ fragment 1F7W NMR - - U/B 1FC2 2.80 Fc fragment Protein A - - - - B/B 1FCC 3.50 Fc fragment Protein G 1H3V 3.10 - - U/B 1IAR 2.60 IL-4 receptor IL-4 - - 1HIK 2.60 B/U 1JCK 3.50 T-cell antigen receptor SEC3 1BEC 1.70 1CK1 2.60 U/U 1JRH 2.80 Antibody A6 Interferon-γ receptor - - - - B/B 1JTD 2.30 TEM-1 β-lactamase BLIP 1ZG4 1.55 - - U/B 1NMB 2.50 NC10 Neuraminidase N9 - - 7NN9 2.00 B/U 2PTC 1.90 Trypsin BPTI 1S0Q 1.02 1G6X 0.86 U/U 1VFB 1.80 Antibody D1.3 HEL - - 3LZT 0.92 B/U a PDB Code, b Resolution in Å; c B, Bound; U, Unbound For most of the complexes, the structure of only one of the two partners is available in the unbound conformation.

This dataset (Table 1 ) includes enzymes-ligand/inhibitor complexes (PDB code: 1JTD , 1BRS , 1BXI , 1A4Y , 1DFJ , 2DAN , 2PTC ), antibody-antigen complexes (PDB code: 1DN2 , 1FCC , 3HFM , 1FC2 , 1NMB , 1AHW , 1VFB , 1JRH , 1JCK ) and other types of interaction (PDB code: 1IAR , 1AIE , 1F47 , 1CG1 , 1A22 ).

Publication Year: 2008


Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces.

(2008) BMC Bioinformatics 9

PubMed: 18939984 | PubMedCentral: PMC2596146 | DOI: 10.1186/1471-2105-9-448

Protein A Protein B ΔG (kJ/mole) PDB Ref BPTI Chymotrypsin -44.96 1CBW [ 49 ] Barnase Barstar -79.50 1B27 [ 50 ] Subtilisin Carlsberg OMTKY3 -59.31 1R0R [ 51 ] Rap1A Raf1 -35.98 1C1Y [ 52 ] Ra... Byr2 -38.45 1K8R [ 53 ] Fv D1.3 Fv E5.2 -45.48 1DVF [ 54 ] Fv D1.3 HEWL -45.10 1VFB [ 55 ] BPTI Trypsin -75.16 2PTC [ 49 ] HyHEL10 Fab HEWL -56.21 3HFM [ 56 ] RalGDS Ras -35.15 1LFD [ 57 ] Subtilisin Carlsberg Eglin C -54.76 1CSE [ 58 ] IM9 Colicin E9 -78.62 1EMV [ 59 ] HyHEL5 Fab HEWL -59.36 1YQV [ 60 ] SGPB OMTKY3 -61.45 3SGB [ 61 ] Ribonuclease Inhibitor Angiogenin -87.15 1A4Y [ 62 ] N9 Neuraminidase NC10 Fab -48.50 1NMB [ 63 ] Subtilisin BPN' SSI -61.33 2SIC [ 64 ] Thrombin Thrombomodulin -53.09 1DX5 [ 65 ] Ribonuclease A Ribonuclease Inhibitor -76.30 1DFJ [ 62 ] Kallikrein A BPTI -51.83 2KAI [ 66 ] Protein constituents of the complexes are given, with the following abbreviations: OMTKY3, turkey ovomucoid third domain; HEWL, Hen Egg White Lysozyme; BPTI, Bovine Pancreatic Trypsin Inhibitor; IM9, Immunity Protein 9; SGPB Streptomyces griseus protease B; SSI, Streptomyces Subtilisin Inhibitor.

Publication Year: 2008


'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces.

(2009) Bioinformatics 25

PubMed: 19179356 | PubMedCentral: PMC2654803 | DOI: 10.1093/bioinformatics/btp058

However, only 13 of them are matched with PDB entries: 1a4y, 1ahw, 1brs, 1bxi, 1cbw, 1dan, 1dvf, 1gc1, 1jck, 1vfb, 2ptc, 2hfm and 3hhr.

Numbers of very warm and hot residues of the 13 protein complexes stored in ASEdb in comparison to those contained in our biclique patterns PDB ΔΔ G ≥1.5 kcal/mol ΔΔ G ≥2.0 kcal/mol ASEdb Biclique ASEdb Biclique 1A4Y 4 4 3 3 1AHW 1 1 1 1 1BRS 10 9 9 8 1BXI 7 7 6 6 1CBW 1 1 1 1 1DAN 6 6 3 3 1DVF 19 18 8 8 1GC1 1 0 0 0 1JCK 6 5 4 4 1VFB 6 5 3 3 2PTC 1 1 1 1 3HFM 6 5 5 4 3HHR 14 11 8 7 Total 82 73 52 49 sensitivity 73/82=89% 49/52=94% The larger ΔΔ G the residues are, more likely those are in our biclique patterns.

Publication Year: 2009


A feature-based approach to modeling protein-protein interaction hot spots.

(2009) Nucleic Acids Res 37

PubMed: 19273533 | PubMedCentral: PMC2677884 | DOI: 10.1093/nar/gkp132

Structural comparison between the unbound and bound states for various proteins using combinatorial extension Bound state a Unbound state b RMSD(Å) c Seq. PDB id Chain id PDB id Chain id ident... ty (%) Angiogenin 1a4y B 1un3 A 0.76 99.1 hGH 1a22 A 1hgu – d 2.68 68.4 Tissue factor e 1ahw C 1tfh A 1.39 100.0 Barnase 1brs A 1bnf A 1.12 98.1 Barstar 1brs D 1a19 A 0.44 98.9 BPTI 1cbw D 1bpt – d 0.39 98.2 Tissue factor e 1dan T 1tfh A 0.63 100.0 RNase inhibitor 1dfj I 2bnh – d 1.50 100.0 CD4 1gc1 C 1cdj A 1.09 100.0 Hen egg lysozyme e 1vfb C 1lyz – d 1.11 100.0 Trypsin 2ptc I 1bpt – d 0.36 98.2 Lysozyme e 3hfm Y 1lyz – d 0.67 100.0 a A protein is in the bound state.

The 17 protein–protein complexes analyzed PDB id First molecule Second molecule 1a4y RNase inhibitor Angiogenin 1a22 Human growth hormone Human growth hormone binding protein 1ahw Immunoglobulin Fab5G9 Tissue factor 1brs Barnase Barstar 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 1cbw BPTI Trypsin inhibitor Chymotrypsin 1dan Blood coagulation factor VIIA Tissue factor 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 1f47 Cell division protein ZIPA Cell division protein FTSZ 1fc2 Fc fragment Fragment B of protein A 1fcc Fc (IGG1) Protein G 1gc1 Envelope protein GP120 CD4 1jrh Antibody A6 Interferon-gamma receptor 1nmb N9 Neuramidase Fab NC10 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 2ptc BPTI Trypsin 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 An independent test set An independent test set is constructed from the BID ( 35 ) to further validate our SVM model.

Publication Year: 2009


A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.

(2009) Bioinformatics 25

PubMed: 19478004 | PubMedCentral: PMC2687974 | DOI: 10.1093/bioinformatics/btp220

PDB chains used for deriving the background distribution for SOIPPA score statistics PDB ID Chain ID CATH ID 1YOZ A 1.10.3200 1YO7 A 1.20.1440 1B3U A 1.25.10 1PPR A 1.40.10 1AGM A 1.50.10 1MVF C 2.10.... 60 1C3K A 2.100.10 1N7V A 2.105.10, 2.60.330, 2.70.250 1GEN A 2.110.10 1GYD A 2.115.10 1A14 A 2.120.10 1A0R A 2.130.10 1AOM A 2.140.10 1P9H A 2.150.10 1EWW A 2.160.10 1T2R B 2.170.260 1MKN A 2.20.60 1YDU A 2.30.240 1XKC A 2.40.320 1KSA A 2.50.10 1ABR B 2.80.10 1B2P A 2.90.10 1VKB A 3.10.490 1BP1 A 3.15.10 1YBE A 3.20.140 2SIC C 3.30.350 1Y0K A 3.40.1540 1J7G A 3.50.80 1J5U A 3.55.10 2PVA A 3.60.60 1A2N A 3.65.10 1AXC A 3.70.10 1BWD A 3.75.10 1A4Y A 3.80.10 1YB5 A 3.90.180 4MT2 A 4.10.10 The residues from the above structures were randomly shuffled 100 times to construct a total of 3600 structural models.

Publication Year: 2009


APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.

(2010) BMC Bioinformatics 11

PubMed: 20377884 | PubMedCentral: PMC2874803 | DOI: 10.1186/1471-2105-11-174

Table 1 Training set of protein structures PDB First molecule Second molecule 1a4y Angiogenin Ribonuclease Inhibitor 1a22 Human growth hormone Human growth hormone binding protein 1ahw Immunoglobulin ... ab 5G9 Tissue factor 1brs Barnase Barstar 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 1cbw BPTI Trypsin inhibitor Chymotrypsin 1dan Blood coagulation factor VIIA Tissue factor 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 1fc2 Fc fragment Fragment B of protein A 1fcc Fc (IGG1) Protein G 1gc1 Envelope protein GP120 CD4 1jrh Antibody A6 Interferon-gamma receptor 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 2ptc BPTI Trypsin 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 Independent test set An independent test set was extracted from the BID database [ 11 ] to further assess the performance of our proposed method.

Publication Year: 2010


DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions.

(2010) Nucleic Acids Res 38

PubMed: 20511591 | PubMedCentral: PMC2896140 | DOI: 10.1093/nar/gkq471

To perform a leave-homologous-complexes-out cross-validation, we skipped all ribonuclease-like complexes (PDB ID’s: 1A4Y and 1DFJ) from the dataset and predicted ΔΔ G values fo... them using adapted potentials derived from the rest of the dataset.

The average experimental uncertainty for 78 (PDB codes of the corresponding complexes: 1a22, 1a4y, 1bxi, 1dfj, 3hfm) of the 309 mutations amounts to 0.31 kcal mol −1 .

Publication Year: 2010


DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts.

(2011) BMC Syst Biol 5 Suppl 1

PubMed: 21689480 | PubMedCentral: PMC3121121 | DOI: 10.1186/1752-0509-5-S1-S5

ASP-435, a residue of ribonuclease inhibitor (in yellow) in ribonuclease inhibitor-angiogenin (in green) complex [PDB:1A4Y] that we have successfully classified as a hot spot residue while Robetta, Fo... dX, EGAD and MINERVA failed.

Publication Year: 2011


Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif.

(2011) PLoS One 6

PubMed: 21961043 | PubMedCentral: PMC3178540 | DOI: 10.1371/journal.pone.0024712

t001 Table 1 Water metrics for human placental RNase inhibitor (hRI)- human angiogenin (hAng) complex (PDB 1a4y, 2.00 Å).

Figure 1 illustrates the set of 16 unique water molecules for the human placental RNase inhibitor (hRI)- human angiogenin (hAng) complex (PDB 1a4y, 2.00 Å) [83] , while Figure 2 displays the same (17 unique waters) for the human TGFβ Type II receptor extracellular domain (hβIIR)-TGF β3 complex (PDB 1ktz, 2.15 Å) [86] .

Publication Year: 2011


A phylogenetic analysis of the globins in fungi.

(2012) PLoS One 7

PubMed: 22384087 | PubMedCentral: PMC3287990 | DOI: 10.1371/journal.pone.0031856

Although the C-terminal 185 residues remain unidentified, the N-terminal (20–560) exhibits a high Z = 30.5 in a FUGUE search [31] with a composite profile of the ribonuclease i... hibitors from Sus scrofa, Homo sapiens and Schizosaccharomyces pombe (PDB: 2bnh, 1a4y, 1yrg, respectively).

Publication Year: 2012


Versatility and invariance in the evolution of homologous heteromeric interfaces.

(2012) PLoS Comput Biol 8

PubMed: 22952442 | PubMedCentral: PMC3431345 | DOI: 10.1371/journal.pcbi.1002677

(A–C) The mutually interologous interfaces are interfaces in Homo sapiens between a conserved partner (ribonuclease inhibitor, in shades of blue) and three different partners with 30% to 38% m... tual interface sequence identity (in green, light green and dark green; respective PDB ids of the complexes 1a4y, 2bex, 1z7x).

The frames show a conserved lysine in the blue chains (K320 in chains A of 1a4y and 2bex and chain W of 1z7x) involved in three different environments: (A) an interface salt bridge, (B) a network of interface hydrogen bonds and (C) no interface contact but a hydrogen bond with interface water.

Publication Year: 2012


A semi-supervised boosting SVM for predicting hot spots at protein-protein interfaces.

(2012) BMC Syst Biol 6 Suppl 2

PubMed: 23282146 | PubMedCentral: PMC3521187 | DOI: 10.1186/1752-0509-6-S2-S6

PDB 1st Molecule 2nd Molecule H NH 1a4y Angiogenin Ribonuclease Inhibitor 3 12 1a22 Human growth hormone Human growth hormone binding protein 7 29 1ahw Immunoglobulin Fab 5G9 Tissue factor 1 3 1brs Ba... nase Barstar 8 1 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 6 3 1cbw BPTI Trypsin inhibitor Chymotrypsin 1 4 1dan Blood coagulation factor VIIA Tissue factor 2 9 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 6 1 1fc2 Fc fragment Fragment B of protein A 1 0 1fcc Fc (IGG1) Protein G 4 2 1gc1 Envelope protein GP120 CD4 0 11 1jrh Antibody A6 Interferon-gamma receptor 8 5 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 3 6 2ptc BPTI Trypsin 1 0 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 11 6 H stands for Hot Spot and NH stands for Non-Hot Spot .

Publication Year: 2012


Crystal structures of murine angiogenin-2 and -3-probing 'structure--function' relationships amongst angiogenin homologues.

(2013) FEBS J 280

PubMed: 23170778 | PubMedCentral: PMC3572582 | DOI: 10.1111/febs.12071

In hAng, this loop contains residues G85 and G86, which have been shown to interact with human RI (PDB code: 1A4Y) 23 .

Publication Year: 2013


Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens.

(2013) BMC Plant Biol 13

PubMed: 23497186 | PubMedCentral: PMC3626623 | DOI: 10.1186/1471-2229-13-43

The homo-dimer conformation of GmRLK18-1 was generated using the software package XtalView, according to the relative position of the homo-dimer conformation of a Ribonuclease inhibitor-angiogenin com... lex (1a4y).

This modeling was based on either the crystal dimer from decorin template [ 21 ] or an amino-peptidase or the RI dimer complexed with angiogenin (1a4y) [ 23 ].

Publication Year: 2013


Crystal structure of human angiogenin with an engineered loop exhibits conformational flexibility at the functional regions of the molecule.

(2013) FEBS Open Bio 3

PubMed: 23772376 | PubMedCentral: PMC3668512 | DOI: 10.1016/j.fob.2012.12.003

The structural superposition of native EDN (PDB: 1GQV [ 62 ]), EDN-RI (PDB: 2BEX [ 41 ]), native ANG (PDB: 4AOH [ 21 ]), ANG–RI (PDB: 1A4Y [ 39 ]) against AEH molecules show that the conformat... onal changes observed are unique to AEH molecules.

In pale cyan is native ANG, light brown is ANG bound to RI (PDB ID: 1A4Y) and in limon is AEH.

However, the structures of ANG in complex with – (a) a leucine rich, natural protein inhibitor (50 kDa) of ANG (the ribonuclease inhibitor – RI; [ 39 ]; PDB ID: 1A4Y) and (b) an antibody fragment 26-2F (shown to inhibit ANG) ([ 40 ]; PDB id: 1H0D) have shown significant conformational changes at the cell-binding region of ANG.

Fig. 3 Cartoon representation of AEH molecule docked to ribonuclease inhibitor (RI – PDB id: 1A4Y).

Publication Year: 2013