scholarly journals Structures of new crystal forms ofMycobacterium tuberculosispeptidyl-tRNA hydrolase and functionally important plasticity of the molecule

2012 ◽  
Vol 68 (2) ◽  
pp. 124-128 ◽  
Author(s):  
M. Selvaraj ◽  
Rais Ahmad ◽  
Umesh Varshney ◽  
M. Vijayan
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Peptide Binding ◽  
Protein Molecule ◽  
Solution Nmr ◽  
Crystal Forms ◽  
X Ray ◽  
Peptide Binding Site ◽  
Different Sources ◽  
Trna Binding

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase fromM. tuberculosisreported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

scholarly journals Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9

2020 ◽  
Author(s):  
D. R. Littler ◽  
B. S. Gully ◽  
R. N. Colson ◽  
J Rossjohn
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Peptide Binding ◽  
Structural Protein ◽  
Dimer Interface ◽  
X Ray ◽  
3C Protease ◽  
Peptide Binding Site ◽  
High Level ◽  
Viral Genomic Rna

AbstractMany of the proteins produced by SARS-CoV-2 have related counterparts across the Severe Acute Respiratory Syndrome (SARS-CoV) family. One such protein is non-structural protein 9 (Nsp9), which is thought to mediate both viral replication and virulence. Current understanding suggests that Nsp9 is involved in viral genomic RNA reproduction. Nsp9 is thought to bind RNA via a fold that is unique to this class of betacoronoaviruses although the molecular basis for this remains ill-defined. We sought to better characterise the SARS-CoV-2 Nsp9 protein and subsequently solved its X-ray crystal structure, in an apo-form and, unexpectedly, in a peptide-bound form with a sequence originating from a rhinoviral 3C protease sequence (LEVL). The structure of the SARS-CoV-2 Nsp9 revealed the high level of structural conservation within the Nsp9 family. The exogenous peptide binding site is close to the dimer interface and impacted on the relative juxtaposition of the monomers within the homodimer. Together we have established a protocol for the production of SARS-CoV-2 Nsp9, determined its structure and identified a peptide-binding site that may warrant further study from the perspective of understanding Nsp9 function.

scholarly journals CR3 (CD11b/CD18) expresses one binding site for Arg-Gly-Asp-containing peptides and a second site for bacterial lipopolysaccharide.

1989 ◽  
Vol 169 (1) ◽  
pp. 175-183 ◽  
Author(s):  
S D Wright ◽  
S M Levin ◽  
M T Jong ◽  
Z Chad ◽  
L G Kabbash
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Synthetic Peptides ◽  
Polymorphonuclear Leukocytes ◽  
Peptide Binding ◽  
Bacterial Lipopolysaccharide ◽  
Peptide Binding Site

Polymorphonuclear leukocytes (PMN) from three patients deficient in the CD18 family of receptors (LFA-1, CR3, and p150,95) exhibited an inability to bind erythrocytes coated with C3bi or bacterial LPS. These observations confirm that the CD18 family, and CR3 in particular, can bind the structurally dissimilar molecules C3bi and LPS. Further studies showed that LPS and C3bi bind to CR3 at distinct sites. mAb OKM10 against CR3 blocked binding of C3bi to PMN but did not block the binding of LPS. In contrast, mAb 904, directed against a different epitope on CR3, blocked binding of LPS to PMN but not binding of C3bi, thus suggesting that different regions of CR3 were involved in binding these two ligands. In addition, synthetic peptides based on the sequence in C3bi recognized by CR3 competitively blocked the binding of C3bi to CR3 but did not block the binding of LPS. Rather, occupation of the peptide binding site on CR3 by the synthetic peptides enhanced binding of LPS. These results indicate that CR3 has two distinct binding sites, one that recognizes ligands composed of protein and a second that recognizes LPS.

Rapid Elaboration of Fragments into Leads Applied to Bromodomain-3 Extra Terminal Domain

2020 ◽  
Author(s):  
Luke Adams ◽  
Lorna E. Wilkinson-White ◽  
Menachem J. Gunzburg ◽  
Stephen J. Headey ◽  
Martin J. Scanlon ◽  
...  
Keyword(s):  
Binding Site ◽  
Systematic Approach ◽  
Structural Information ◽  
Peptide Binding ◽  
Chemical Diversity ◽  
Chemical Probes ◽  
Protein Targets ◽  
Structure Activity ◽  
Peptide Binding Site ◽  
Selection Of

The development of low-affinity fragment hits into higher affinity leads is a major hurdle in fragment-based drug design. Here we demonstrate an approach for the Rapid Elaboration of Fragments into Leads (REFiL) applying an integrated workflow that provides a systematic approach to generate higher-affinity binders without the need for structural information. The workflow involves the selection of commercial analogues of fragment hits to generate preliminary structure-activity relationships. This is followed by parallel microscale chemistry using chemoinformatically designed reagent libraries to rapidly explore chemical diversity. Upon completion of a fragment screen against Bromodomain-3 extra terminal (BRD3-ET) domain we applied the REFiL workflow, which allowed us to develop a series of tetrahydrocarbazole ligands that bind to the peptide binding site of BRD3-ET. With REFiL we were able to rapidly improve binding affinity >30-fold. The REFiL workflow can be applied readily to a broad range of protein targets without the need of a structure, allowing the efficient evolution of low-affinity fragments into higher affinity leads and chemical probes.<br>

Solubilization and Characterization of Calcitonin Gene-Related Peptide Binding Site from Porcine Spinal Cord

1988 ◽  
Vol 50 (2) ◽  
pp. 480-485 ◽  
Author(s):  
Osamu Hiroshima ◽  
Yoshihisa Sano ◽  
Teruaki Yuzuriha ◽  
Chiyuki Yamato ◽  
Akira Saito ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Binding Site ◽  
Peptide Binding ◽  
Calcitonin Gene Related Peptide ◽  
Related Peptide ◽  
Calcitonin Gene ◽  
Peptide Binding Site

The Crystal Structures of the SH2 Domain of p56lckComplexed with Two Phosphonopeptides Suggest a Gated Peptide Binding Site

1995 ◽  
Vol 246 (2) ◽  
pp. 344-355 ◽  
Author(s):  
Vincent Mikol ◽  
Götz Baumann ◽  
Thomas H. Keller ◽  
Ute Manning ◽  
Mauro G.M. Zurini
Keyword(s):  
Binding Site ◽  
Crystal Structures ◽  
Peptide Binding ◽  
Sh2 Domain ◽  
Peptide Binding Site

Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii

2020 ◽  
Vol 76 (5) ◽  
pp. 447-457
Author(s):  
Ping Huang ◽  
Shiwang Wu ◽  
Shaoqing Yang ◽  
Qiaojuan Yan ◽  
Zhengqiang Jiang
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Structural Basis ◽  
Carbohydrate Binding ◽  
Type I ◽  
Debranching Enzyme ◽  
Crystal Forms ◽  
Aromatic Residues ◽  
Starch Debranching Enzyme ◽  
Paenibacillus Barengoltzii

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

Characterisation of Metal Binding Sites for 8-Azaguanine and 8-Azahypoxanthine Derivatives Synthesis and X-Ray Structural Analysis of Methylmercury(II) and Zinc(II) Complexes

1986 ◽  
Vol 41 (9) ◽  
pp. 1117-1122 ◽  
Author(s):  
W. S. Sheldrick ◽  
P. Bell
Keyword(s):  
Structural Analysis ◽  
Binding Site ◽  
Metal Binding ◽  
Binding Sites ◽  
Antineoplastic Agent ◽  
X Ray ◽  
Metal Binding Sites ◽  
Ph Values ◽  
Ph Range

Abstract The complexes [(CH3Hg)AGuaH ] (1) and [(CH3Hg)2AGua] • H2O (2) have been isolated from aqueous 1:1 and 2:1 solutions of CH3HgOH and 8 -azaguanine (AGuaH2) at respective pH values of 5 and 9. Only one CH3Hg+ complex of 8 -azahypoxanthine (AHxH2), namely [(CH3Hg)2AHx] (3), could be isolated under analogous conditions. X-ray structural analyses established N1 and N9 as metal binding sites in 3 and N9 as the coordination position in [Zn(H2O)4(AHxH)2] (4). With 8-aza-9-benzylhypoxanthine (9-BzAHxH) only one CH3Hg+ complex [(CH3Hg)9-BzAHx] (5) could be isolated in the pH range 2-10. N1 was established by X-ray structural analysis as the binding site. The relevance o f these findings to an understanding of ligand behaviour of the antineoplastic agent 8 -azaguanine is discussed.

Autoradiographic localization of a novel peptide binding site in rat brain using the substance P analog, eledoisin

Neuropeptides ◽  
1984 ◽  
Vol 4 (4) ◽  
pp. 343-349 ◽  
Author(s):  
Richard B. Rothman ◽  
Janine A. Danks ◽  
Miles Herkenham ◽  
Margaret A. Cascieri ◽  
Gary G. Chicchi ◽  
...  
Keyword(s):  
Substance P ◽  
Binding Site ◽  
Rat Brain ◽  
Peptide Binding ◽  
Peptide Binding Site

scholarly journals Sequence-selective DNA binding with cell-permeable oligoguanidinium–peptide conjugates

2015 ◽  
Vol 51 (23) ◽  
pp. 4811-4814 ◽  
Author(s):  
Jesús Mosquera ◽  
Mateo I. Sánchez ◽  
Julián Valero ◽  
Javier de Mendoza ◽  
M. Eugenio Vázquez ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Peptide Binding ◽  
Peptide Fragment ◽  
Peptide Conjugates ◽  
Bzip Protein ◽  
Short Peptide ◽  
Peptide Binding Site ◽  
Selective Dna Binding

Conjugation of a short peptide fragment from a bZIP protein to an oligoguanidinium tail results in a DNA-binding miniprotein that selectively interacts with composite sequences containing the peptide-binding site next to an A/T-rich tract.

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