Abstract
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. The web server is freely available at http://202.41.10.46/calb/index.html.
Highlights
Calcium signaling plays a major role in controlling most biological systems and many cellular functions, such as fertilization, motility, cell differentiation, proliferation and apoptosis, which are directly or indirectly regulated by Ca2+ [1,2,3]
A few experimental methods based on biophysical techniques, such as Isothermal titration calorimetry (ITC) surface plasmon resonance (SPR) & fluorescence [26] are available for determination of Ca2+-binding parameters
Position-specific scoring matrix After obtaining position-specific scoring matrix (PSSM) scores using equations (1) and (2) for all the sequences obtained from the literature, we calculated the correlation coefficient between the experimental affinity constants (Ka) and PSSM to be 0.61 (Figure S1 in File S1)
Summary
Calcium signaling plays a major role in controlling most biological systems and many cellular functions, such as fertilization, motility, cell differentiation, proliferation and apoptosis, which are directly or indirectly regulated by Ca2+ [1,2,3]. Ca2+ is bound by a variety of proteins that are capable of binding with different affinities [7,8,9]. Such calcium binding proteins (CaBPs) can be classified into two categories, Ca2+ sensors and buffers. An EF hand is composed of a typical helix-loop-helix structural unit This group is the largest and includes well-known members, such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site [13]. Proteins, such as calbindin D9k do not undergo calcium-dependent conformational changes [15,16,17]
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