Comparison of protein structures using 3D profile alignment

Suyama, Mikita; Matsuo, Yo; Nishikawa, Ken

doi:10.1007/pl00000065

Cited by 30 publications

(19 citation statements)

References 36 publications

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“…A number of alternative strategies have been developed. These include template consensus sequences [41][42] and profile analysis [43][44][45]. All these approaches, based on either multiple sequence or structure alignments, are more sensitive because the consensus sequences are better representative of the sequence family, and the profile reflects the conserved structural or functional preferences.…”

Section: Homologue Detection and Alignmentmentioning

confidence: 99%

Advances in Homology Protein Structure Modeling

Xiang

2006

CPPS

413

243

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Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the overwhelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function.

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Section: Homologue Detection and Alignmentmentioning

confidence: 99%

Advances in Homology Protein Structure Modeling

Xiang

2006

CPPS

413

243

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“…It was possible to derive the tertiary structure of the three DBDs by homology modelling. After 3000 steps of steep descent energy minimization, the structures of molded DBDs were evaluated by the profile-3D (Suyama et al, 1997). Figure 2A shows that the compatibility scores of residues were above zero, which meant that these residues were folded reasonably, except for the four C-terminal residues of AtEBP and AtERF4.…”

Section: Resultsmentioning

confidence: 99%

Molecular dynamics simulations reveal the disparity in specific recognition of GCC‐box by AtERFs transcription factors super family in Arabidopsis

Wang

Yang

Yin

et al. 2009

J of Molecular Recognition

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Arabidopsis ethylene responsive element binding factors (AtERFs) form a transcription factor super family. While the functions of most AtERFs are unknown, a number of AtERFs appear to be involved in regulation of stress-related genes through their DNA binding domains (DBD), namely ERF domains, which recognize a consensus motif GCC-box at the regulatory region. In this study, molecular dynamics simulations were performed on the four ERF domain-GCC-box complexes, AtERF1, AtERF4, AtEBP and CFBF1, to determine disparity in specific binding to the GCC-box by the AtERFs. Our results suggested that three amino acid residues Arg29, Glu39 and Arg41, played a vital role in direct readout of DNA. The position of the consensus sequence GCCGCC has an intrinsic disparity on binding with ERF domains. The third C, fourth G and the last C in the GCC motif was compulsory for recognition by ERF domains. Our results provide structural evidence for a sequence-dependent recognition mechanism for AtERFs.

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“…were generated by the I-TASSER web server (Wu, 2007;Zhang, 2008;Roy et al, 2010;Yang et al, 2013) and evaluated by VERIFY 3D (http://services.mbi. ucla.edu/Verify_3D/) (Eisenberg et al, 1997), 3-D profile analysis (Suyama et al, 1997), and Errat (MacArthur et al, 1994;Gundampati et al, 2012) to check the quality of the overall fold/structure, errors over localized regions, and stereochemical parameters such as bond lengths and angles. Structural validations of target protein models were done by PROCHECK (Laskowski et al, 1993), which determines stereochemical aspects along with main chain and side chain parameters with a comprehensive analysis.…”

Section: Homology Modeling and Identification Of Functional Sitementioning

confidence: 99%

Modeling of PrnD protein from Pseudomonas fluorescens RajNB11 and its comparative structural analysis with PrnD proteins expressed in Burkholderia and Serratia

Singh¹,

Singh²,

Sharma³

et al. 2016

Turk J Biol

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Pyrrolnitrin is produced by Pseudomonas fluorescens and plays an important role in control of pathogenic fungi. The prnABCD gene cluster codes for enzymes involved in biosynthesis of pyrrolnitrin. Among the four genes, prnD is very important as it codes for arylamine N-oxygenase, the only biochemically characterized oxygenase involved in oxidation of the amino group of aminopyrrolnitrin to a nitro group to form pyrrolnitrin. A strain of Pseudomonas fluorescens RajNB11 efficient for antifungal activity was found to produce pyrrolnitrin. The prnD gene product of P. fluorescens RajNB11 that catalyzes the final step of production of pyrrolnitrin was characterized in the present study with regards to its stability and catalytic activity. The prnD gene was amplified from RajNB11, sequenced, translated, and 3-D modeled to its protein structure. The modeled protein of the test organism was compared to PrnD proteins of Burkholderia sp. and Serratia sp. The protein from P. fluorescens was found to be basic, hydrophilic with higher thermal stability, and easily separated after expression and purification. The protein of P. fluorescens was found to have a better folded structure, more serine residues in the active site, and better active site properties and isoelectric point value in comparison to PrnD proteins of Burkholderia and Serratia.

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Comparison of protein structures using 3D profile alignment

Cited by 30 publications

References 36 publications

Advances in Homology Protein Structure Modeling

Advances in Homology Protein Structure Modeling

Molecular dynamics simulations reveal the disparity in specific recognition of GCC‐box by AtERFs transcription factors super family in Arabidopsis

Modeling of PrnD protein from Pseudomonas fluorescens RajNB11 and its comparative structural analysis with PrnD proteins expressed in Burkholderia and Serratia

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