A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures

Carugo, Oliviero; Pongor, Sándor

doi:10.1110/ps.690101

Cited by 321 publications

(234 citation statements)

References 13 publications

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“…We superimposed the template and model structures, and calculated a root-mean-square deviation value of 0.672 Å over a total of 383 aligned residues (Fig. 1b), indicating a high degree of similarity between structures (Carugo & Pongor, 2001). …”

Section: Methodsmentioning

confidence: 99%

MgtE is a dual-function protein in Pseudomonas aeruginosa

2014

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The opportunistic pathogen Pseudomonas aeruginosa causes a wide range of infections, including chronic biofilm infections in the lungs of individuals with cystic fibrosis. We previously found that the inner-membrane protein MgtE can function both as a magnesium transporter and a virulence modulator, although the exact mechanism governing these activities is unclear. To address this issue, we carried out an experimental characterization of P. aeruginosa MgtE and generated a computer-rendered model. Our in silico analysis demonstrated the structural similarity of P. aeruginosa MgtE to that of the crystal structure of MgtE in Thermus thermophilus. Experimentally, we verified that MgtE is not essential for growth and found that it may not be involved directly in biofilm formation, even under low-magnesium conditions. We demonstrated both magnesium transport and cytotoxicity-regulating functions, and showed that magnesiumbinding sites in the connecting helix region of MgtE are vital in coupling these two functions. Furthermore, limiting magnesium environments stimulated mgtE transcriptional responses. Our results suggested that MgtE might play an important role in linking magnesium availability to P. aeruginosa pathogenesis.

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Section: Methodsmentioning

confidence: 99%

MgtE is a dual-function protein in Pseudomonas aeruginosa

2014

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“…In sequence similarity, a technique called homology modeling is used based on the structure of a known protein as a template to predict the structure of an unknown protein [3]. If structural information of the protein exists, there are methods that have been developed to compare the structures [4][5][6][7][8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

A new definition and properties of the similarity value between two protein structures

Fathi

2016

J Biol Phys

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Knowledge regarding the 3D structure of a protein provides useful information about the protein's functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein's atoms and concentrate on the number of protein's atoms to be compared. This defines a new measure, called the weighted similarity value (WSV), adding physical properties to geometrical properties. We also show that our results are in good agreement with the results obtained by TM-SCORE and DALILITE. WSV can be of use in protein classification and in drug discovery.

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“…For this section, our RMSD calculation is based on the Cartesian coordinates of the Cα atoms of the two proteins and it ignores side chain atoms for comparison purposes. Given by (Carugo and Pongor, 2001), the RMSD is defined to be:…”

Section: Methodsologymentioning

confidence: 99%

Improved scatter search algorithm for predicting all-atoms protein structures using charmm22 energy model. (c2010)

Ghalayini¹

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A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures

Cited by 321 publications

References 13 publications

MgtE is a dual-function protein in Pseudomonas aeruginosa

MgtE is a dual-function protein in Pseudomonas aeruginosa

A new definition and properties of the similarity value between two protein structures

Improved scatter search algorithm for predicting all-atoms protein structures using charmm22 energy model. (c2010)

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