Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.

The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca²⁺ displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amin...

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Autores principales:	Mohit Mazumder, Narendra Padhan, Alok Bhattacharya, Samudrala Gourinath
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c66ac7c97e114588b575c33bd0ceddb1
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spelling	oai:doaj.org-article:c66ac7c97e114588b575c33bd0ceddb12021-11-18T08:21:38ZPrediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.1932-620310.1371/journal.pone.0096202https://doaj.org/article/c66ac7c97e114588b575c33bd0ceddb12014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24760183/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca²⁺ displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amino acid patterns of canonical EF hand sequences obtained from available crystal structures were used to develop a classifier that distinguishes Ca²⁺-binding loops and non Ca²⁺-binding regions with 100% accuracy. To investigate further, we performed a proteome-wide prediction for E. histolytica, and classified known EF-hand proteins. We compared our results with published methods on the E. histolytica proteome scan, and demonstrated our method to be more specific and accurate for predicting potential canonical Ca²⁺-binding loops. Furthermore, we annotated canonical EF-hand motifs and classified them based on their Ca²⁺-binding affinities using support vector machines. Using a novel method generated from position-specific scoring metrics and then tested against three different experimentally derived EF-hand-motif datasets, predictions of Ca²⁺-binding affinities were between 87 and 90% accurate. Our results show that the tool described here is capable of predicting Ca²⁺-binding affinity constants of EF-hand proteins.Mohit MazumderNarendra PadhanAlok BhattacharyaSamudrala GourinathPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 4, p e96202 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mohit Mazumder Narendra Padhan Alok Bhattacharya Samudrala Gourinath Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.
description	The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca²⁺ displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amino acid patterns of canonical EF hand sequences obtained from available crystal structures were used to develop a classifier that distinguishes Ca²⁺-binding loops and non Ca²⁺-binding regions with 100% accuracy. To investigate further, we performed a proteome-wide prediction for E. histolytica, and classified known EF-hand proteins. We compared our results with published methods on the E. histolytica proteome scan, and demonstrated our method to be more specific and accurate for predicting potential canonical Ca²⁺-binding loops. Furthermore, we annotated canonical EF-hand motifs and classified them based on their Ca²⁺-binding affinities using support vector machines. Using a novel method generated from position-specific scoring metrics and then tested against three different experimentally derived EF-hand-motif datasets, predictions of Ca²⁺-binding affinities were between 87 and 90% accurate. Our results show that the tool described here is capable of predicting Ca²⁺-binding affinity constants of EF-hand proteins.
format	article
author	Mohit Mazumder Narendra Padhan Alok Bhattacharya Samudrala Gourinath
author_facet	Mohit Mazumder Narendra Padhan Alok Bhattacharya Samudrala Gourinath
author_sort	Mohit Mazumder
title	Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.
title_short	Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.
title_full	Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.
title_fullStr	Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.
title_full_unstemmed	Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.
title_sort	prediction and analysis of canonical ef hand loop and qualitative estimation of ca²⁺ binding affinity.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/c66ac7c97e114588b575c33bd0ceddb1
work_keys_str_mv	AT mohitmazumder predictionandanalysisofcanonicalefhandloopandqualitativeestimationofca2bindingaffinity AT narendrapadhan predictionandanalysisofcanonicalefhandloopandqualitativeestimationofca2bindingaffinity AT alokbhattacharya predictionandanalysisofcanonicalefhandloopandqualitativeestimationofca2bindingaffinity AT samudralagourinath predictionandanalysisofcanonicalefhandloopandqualitativeestimationofca2bindingaffinity
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Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity.

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