Gazi Md Amran, Kibria Mohammad Golam, Mahfuz Mustafa, Islam Md Rezaul, Ghosh Prakash, Afsar Md Nure Alam, Khan Md Arif, Ahmed Tahmeed
Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
Gene. 2016 Oct 15;591(2):442-55. doi: 10.1016/j.gene.2016.06.057. Epub 2016 Jul 1.
The global control of tuberculosis (TB) remains a great challenge from the standpoint of diagnosis, detection of drug resistance, and treatment. Major serodiagnostic limitations include low sensitivity and high cost in detecting TB. On the other hand, treatment measures are often hindered by low efficacies of commonly used drugs and resistance developed by the bacteria. Hence, there is a need to look into newer diagnostic and therapeutic targets. The proteome information available suggests that among the 3906 proteins in Mycobacterium tuberculosis H37Rv, about quarter remain classified as hypothetical uncharacterized set. This study involves a combination of a number of bioinformatics tools to analyze those hypothetical proteins (HPs). An entire set of 999 proteins was primarily screened for protein sequences having conserved domains with high confidence using a combination of the latest versions of protein family databases. Subsequently, 98 of such potential target proteins were extensively analyzed by means of physicochemical characteristics, protein-protein interaction, sub-cellular localization, structural similarity and functional classification. Next, we predicted antigenic proteins from the entire set and identified B and T cell epitopes of these proteins in M. tuberculosis H37Rv. We predicted the function of these HPs belong to various classes of proteins such as enzymes, transporters, receptors, structural proteins, transcription regulators and other proteins. However, the structural similarity prediction of the annotated proteins substantiated the functional classification of those proteins. Consequently, based on higher antigenicity score and sub-cellular localization, we choose two (NP_216420.1, NP_216903.1) of the antigenic proteins to exemplify B and T cell epitope prediction approach. Finally we found 15 epitopes those located partially or fully in the linear epitope region. We found 21 conformational epitopes by using Ellipro server as well. In silico methodology used in this study and the data thus generated for HPs of M. tuberculosis H37Rv may facilitate swift experimental identification of potential serodiagnostic and therapeutic targets for treatment and control.
从诊断、耐药性检测和治疗的角度来看，全球结核病（TB）防控仍然是一项巨大挑战。主要的血清学诊断局限包括检测结核病时灵敏度低和成本高。另一方面，治疗措施常常受到常用药物疗效低以及细菌产生耐药性的阻碍。因此，有必要探索更新的诊断和治疗靶点。现有蛋白质组信息表明，在结核分枝杆菌H37Rv的3906种蛋白质中，约四分之一仍被归类为假设的未表征蛋白组。本研究结合多种生物信息学工具来分析这些假设蛋白（HPs）。首先使用最新版本的蛋白质家族数据库组合，对总共999种蛋白质进行筛选，以高可信度筛选具有保守结构域的蛋白质序列。随后，通过理化特性、蛋白质-蛋白质相互作用、亚细胞定位、结构相似性和功能分类，对98种此类潜在靶蛋白进行了广泛分析。接下来，我们从整个蛋白集中预测抗原蛋白，并鉴定这些蛋白在结核分枝杆菌H37Rv中的B细胞和T细胞表位。我们预测这些假设蛋白属于各种蛋白质类别，如酶、转运蛋白、受体、结构蛋白、转录调节因子和其他蛋白质。然而，对注释蛋白的结构相似性预测证实了这些蛋白的功能分类。因此，基于较高的抗原性评分和亚细胞定位，我们选择两种抗原蛋白（NP_216420.1、NP_216903.1）来举例说明B细胞和T细胞表位预测方法。最后，我们发现了15个部分或完全位于线性表位区域的表位。我们还使用Ellipro服务器发现了21个构象表位。本研究中使用的计算机模拟方法以及由此为结核分枝杆菌H37Rv的假设蛋白生成的数据，可能有助于快速实验鉴定用于治疗和控制的潜在血清学诊断和治疗靶点。
