Evolutionary and Molecular Aspects of Indian Tomato Leaf Curl Virus Coat Protein

Abstract

Tomato leaf curl disease (ToLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface, and stunted plant growth caused by tomato leaf curl virus (ToLCV). In the present study, using computational methods we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]), India. We found that the amino acids in coat protein required for systemic infection, viral particle formation, and insect transmission to host cells were conserved amongst Indian strains. Phylogenetic studies on Indian ToLCV coat proteins showed evolutionary compatibility with other viral taxa. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the viral DNA required for encapsidation and nuclear shuttling was investigated through sequence- and structure-based approaches. We further emphasized the role of loops in coat protein structure as molecular recognition interface.

Genome wide molecular evolution analysis of begomoviruses reveals unique diversification pattern in coat protein gene of Old World and New World viruses

“…But in the case of OW viruses the sequence diversification of cp and rep gene has been found to be similar. Previous studies have reported that cp is conserved among geminiviruses, different begomoviruses and in the Indian strain of ToLCV [11,19,25,28,29]. In the present study comparative diversity analysis of the genes in OW and NW viruses has been investigated.…”

“…The results suggest that probably the NLS sequences at N-terminal are gradually disappearing from NW coat proteins and the intracellular [3,13,25,27,57,58]. The NLS motif in coat protein is demonstrated to help in nuclear targeting of the OW viruses like MYMV [13], TYLCV [25], and ACMV [58]. Ha et al [15] have reported that the jute infection CoGMV and CoYVV lacks the second and third basic domain in the N-terminal region of coat protein like some other NW viruses.…”

Molecular Identification and in silico Characterization of Coat Protein in Tomato Leaf Curl Virus Associated in Tomato from South Gujarat Region of India

“…As these procedures yielded one close homologs. So, we choose to go for homology modeling of coat protein using online swiss model web server (https://swissmodel.expasy.org/) (Patel and Kalaria, 2018;kumar et al, 2012).…”

Compound prioritization from inverse docking experiment using receptor‐centric and ligand‐centric methods: a case study on Plasmodium falciparum Fab enzymes

“…Most of the similar ligands score a docking energy within this energy error window (reference molecule docking energy ± 2.63 kcal/mol) making it difficult to prioritize compounds amongst false positive hits. With ongoing efforts on development of computational strategies on medicinal plants based drug discovery, structural bioinformatics and related methods (Kumar et al ., ; Kumar et al ., , ), we propose here a knowledge‐based approach wherein classical docking, quantitative‐structure activity relationship (QSAR) and machine learning models can be efficiently integrated to prioritize compounds from each method and identify a set of common molecule. We used Autodock Vina program (Trott and Olson, ) for docking, VLifeMDS molecular field point‐based 3D QSAR (MFP‐QSAR) for QSAR modelling, and shape and electrostatic similarity descriptors (along with MFP descriptors) to develop multilayer perceptron (MLP) models.…”