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, 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.
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
Mohit
M
Mazumder
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
Narendra
N
Padhan
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
Alok
A
Bhattacharya
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
Samudrala
S
Gourinath
D001665:Binding Sites; D002118:Calcium / Q000737:chemistry / Q000378:metabolism; D002135:Calcium-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004748:Entamoeba histolytica / Q000737:chemistry / Q000378:metabolism*; D056510:Position-Specific Scoring Matrices; D020543:Proteome; D015800:Protozoan Proteins / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship; D060388:Support Vector Machine
D002135:Calcium-Binding Proteins; D020543:Proteome; D015800:Protozoan Proteins; D002118:Calcium