PSAIA – Protein Structure and Interaction Analyzer

Mihel, J.; Šikić, Mile; Tomić, Sanja; Jeren, Branko; Vlahoviček, Kristian

doi:10.1186/1472-6807-8-21

Cited by 174 publications

(120 citation statements)

References 17 publications

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“…Relative accessible surface area (RASA) of the trimer was calculated using the protein structure and interaction analyser (Mihel et al, 2008) with a probe radius of 1.4 Å . We considered an amino acid to be exposed if the RASA of its side chain was above 20.…”

Section: Methodsmentioning

confidence: 99%

Genetic and antigenic characterization of sigma C protein from avian reovirus

Goldenberg¹,

Pasmanik‐Chor²,

Pirak³

et al. 2010

Avian Pathology

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Avian reovirus (ARV) causes viral arthritis, tenosynovitis, liver infection and immunosuppression in birds. Live-attenuated and inactivated vaccines for ARV are available, but do not efficiently protect against recent variants. Sigma C, which mediates virus attachment to target cells, is the most variable protein in ARV. Antibodies to this protein neutralize viral infection. The purpose of the present study was to characterize sigma C in isolates of ARV from infected birds, as compared with the vaccine strain. Amino acids 27 to 293 of sigma C from 28 Israeli isolates were compared, classified and analysed using bioinformatics tools. Large variations were found among the isolates, and the vaccine strain was shown to differ from most of the studied strains, which could explain the failure of commonly used vaccinations in protecting birds against ARV infection. Based on sigma C protein sequences from all over the world, ARV can be divided into four groups. Isolates from all groups were found in the field simultaneously, possibly explaining the insufficient protection achieved by the vaccine strain, which is represented in one of the groups. The results point out the need and the difficulty in producing a wide-ranging vaccine. Several conserved regions among all reported ARV sigma C proteins were identified. These peptides were further studied for structural and functional properties, and for antigenic characterization. The results of this study shed light on peptide selection for a broad and efficient vaccine.

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Section: Methodsmentioning

confidence: 99%

Genetic and antigenic characterization of sigma C protein from avian reovirus

Goldenberg¹,

Pasmanik‐Chor²,

Pirak³

et al. 2010

Avian Pathology

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“…12 The thermodynamic stability of the observed and modeled dimers was evaluated using PSAIA (Protein Structure and Interaction Analyzer) 37 and PISA (Protein Interfaces, Surfaces, and Assemblies). 17 The following dimers were considered: possible dimers in the crystal structures of (1) r-12/15LOX (PDB ID: 2P0M), (2) human engineered 5LOX (PDB ID: 3O8Y), (3) hp-12LOX distorted catalytic domain (PDB ID: 3D3L), and (4) homology models for hp-12LOX formed by A-conformers and Bconformers (observed in PDB ID: 2P0M), including optimization of the interface contacts.…”

Section: Thermodynamic Stability Calculationsmentioning

confidence: 99%

Probing Dimerization and Structural Flexibility of Mammalian Lipoxygenases by Small-Angle X-ray Scattering

Shang

Ivanov

Svergun

et al. 2011

Journal of Molecular Biology

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Human lipoxygenases (LOXs) and their metabolites have a great impact on human homeostasis and are of interest for targeted drug design. This goal requires detailed knowledge of their structures and an understanding of structure-function relationship. At the moment, there are two complete crystal structures for mammalian LOX [rabbit 12/15LOX (r-12/15LOX) and human 5LOX (h-5LOX)] and a fragment of human 12LOX. The low-resolution structures in solution for various LOX isoforms have brought about controversial results. Here we explored the behavior of r-12/15LOX in aqueous solution under different conditions (salt and pH) by small-angle X-ray scattering (SAXS) and compared it with human platelet-type 12S-LOX (hp-12LOX) and h-5LOX. Thermodynamic calculations concerning the stability of molecular assemblies, thermal motion analysis [TLSMD (translation, libration, and screw rotation motion detection based on crystallographic temperature factor B j )], and results of SAXS analyses brought about the following conclusions: (i) in contrast to its crystal structure, r-12/15LOX functions as a monomer that dominates in solution; (ii) it dimerizes at higher protein concentrations in the presence of salt and with increasing degree of motional freedom of the N-terminal PLAT domain, as suggested by the Y98,614→ R double mutant; (iii) in aqueous solutions, hp-12LOX is stable as a dimer, in contrast to h-5LOX and r-12/15LOX, which are monomeric; and (iv) all three *Corresponding author. E-mail address: ewa.skrzypczak-jankun@utoledo.edu. Present address: A. M. Aleem, Biochemistry Department, College of Sciences, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia.Abbreviations used: LOX, lipoxygenase; r-12/15LOX, rabbit 12/15LOX; h-5LOX, human 5LOX; SAXS, small-angle X-ray scattering; hp-12LOX, human platelet-type 12S-LOX; PDB, Protein Data Bank. doi:10.1016/j.jmb.2011.04.035 J. Mol. Biol. (2011

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“…In the FSH-FSHR complex, 16 FSHa chain residues and 13 FSHb chain residues produced interactions O10 Å 2 DASA (difference between ASA values before and after complexation) on complexation with 31 FSHR residues. The DASA values of 1 Å 2 and above are enough to indicate that a residue interacts on complexation; however, for the purpose of this study, values above 10 Å 2 were classed as strong interactions in the interface ( Jones & Thornton 1997, Mihel et al 2008. In the case of TSH-TSHR interactions, 15 TSHa chain residues and 14 TSHb chain residues produced interactions O10 Å 2 DASA on complexation with 31 TSHR residues.…”

Section: Fsh-fshr and Tsh-tshr Interfacesmentioning

confidence: 99%

FSH and TSH binding to their respective receptors: similarities, differences and implication for glycoprotein hormone specificity

Miguel¹,

Sanders²,

Chirgadze³

et al. 2008

Journal of Molecular Endocrinology

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The crystal structures of the leucine-rich repeat domain (LRD) of the FSH receptor (FSHR) in complex with FSH and the TSH receptor (TSHR) LRD in complex with the thyroid-stimulating autoantibody (M22) provide opportunities to assess the molecular basis of the specificity of glycoprotein hormone-receptor binding. A comparative model of the TSH-TSHR complex was built using the two solved crystal structures and verified using studies on receptor affinity and activation. Analysis of the FSH-FSHR and TSH-TSHR complexes allowed identification of receptor residues that may be important in hormone-binding specificity. These residues are in leucine-rich repeats at the two ends of the FSHR and the TSHR LRD structures but not in their central repeats. Interactions in the interfaces are consistent with a higher FSH-binding affinity for the FSHR compared with the binding affinity of TSH for the TSHR. The higher binding affinity of porcine (p)TSH and bovine (b)TSH for human (h)TSHR compared with hTSH appears not to be dependent on interactions with the TSHR LRD as none of the residues that differ among hTSH, pTSH or bTSH interact with the LRD. This suggests that TSHs are likely to interact with other parts of the receptors in addition to the LRD with these non-LRD interactions being responsible for affinity differences. Analysis of interactions in the FSH-FSHR and TSH-TSHR complexes suggests that the a-chains of both hormones tend to be involved in the receptor activation process while the b-chains are more involved in defining binding specificity.

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PSAIA – Protein Structure and Interaction Analyzer

Abstract: Background: PSAIA (Protein Structure and Interaction Analyzer) was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites.

Cited by 174 publications

References 17 publications

Genetic and antigenic characterization of sigma C protein from avian reovirus

Genetic and antigenic characterization of sigma C protein from avian reovirus

Probing Dimerization and Structural Flexibility of Mammalian Lipoxygenases by Small-Angle X-ray Scattering

FSH and TSH binding to their respective receptors: similarities, differences and implication for glycoprotein hormone specificity

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