Biology subjects

Amani, K.

Publications and source records attributed to Amani, K..

3 recordsLinked to original sources

bioRxiv2024

NeuroFold: A Multimodal Approach to Generating Novel Protein Variants in silico

The generation of high-performance enzyme variants with desired physicochemical and functional properties presents a formidable challenge in the field of protein engineering. Existing in silico design methods are limited by inadequate training data, insufficient diversity within datasets, and suboptimal sampling techniques. Here, we introduce a novel approach that addresses these limitations and significantly improves the efficiency of generating functional enzyme variants. Using a multimodal approach, NeuroFold can leverage sequence, structural, and homology data during both sampling and discrimination phases, thereby enabling more diverse and informed sampling of the sequence space. Our model demonstrated a 40-fold increase in Spearman rank correlation as compared to large language models (LLMs) such as ESM-1v and empowers the rapid creation of high-quality enzyme variants, such as the {beta}-lactamase variants generated by NeuroFold in this study, which demonstrated increased thermostability and varying levels of activity. This pipeline represents a promising advancement in the field of enzyme engineering, offering a valuable tool for the development of novel enzymes with enhanced performance and desired chemical properties. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/584504v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@6d8137org.highwire.dtl.DTLVardef@13e6c28org.highwire.dtl.DTLVardef@12ebff6org.highwire.dtl.DTLVardef@3ce466_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors in Solanum lycopersicum (tomato)

Cellular signalling generates calcium (Ca2+) ions, which are ubiquitous secondary messengers decoded by calcium-dependent protein kinases, calcineurins, calreticulin, calmodulins (CAMs) and CAM-binding proteins. Previous studies in the model plant Arabidopsis thaliana have shown the critical roles of the CAM-BINDING PROTEIN 60 (CBP60) protein family in plant growth, stress responses and immunity. Certain CBP60 factors can regulate plant immune responses, like pattern-triggered immunity, effector-triggered immunity, and synthesis of major plant immune-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). Although homologous CBP60 sequences have been identified in the plant kingdom, their function and regulation in most species remain unclear. In this paper, we specifically characterized 11 members of the CBP60 family in the agriculturally important crop tomato (Solanum lycopersicum). Protein sequence analyses revealed that three CBP60 homologs have the closest amino acid identity to Arabidopsis CBP60g and SARD1, master transcription factors involved in plant immunity. Strikingly, AlphaFold deep learning-assisted prediction of protein structures highlighted close structural similarity between these tomato and Arabidopsis CBP60 homologs. Conserved domain analyses revealed that they possess CAM-binding domains and DNA-binding domains, reflecting their potential involvement in linking Ca2+ signalling and transcriptional regulation in tomato plants. In terms of their gene expression profiles under biotic (Pseudomonas syringae pv. tomato DC3000 pathogen infection) and/or abiotic stress (warming temperatures), five tomato CBP60 genes were pathogen-responsive and temperature-sensitive, reminiscent of Arabidopsis CBP60g and SARD1. Overall, we present a genome-wide identification of the CBP60 gene/protein family in tomato plants, and we provide evidence on their regulation and potential function as Ca2+-sensing transcriptional regulators.

plant biology↗

bioRxiv2022

CBP60-DB: An AlphaFold-predicted plant kingdom-wide database of the CALMODULIN-BINDING PROTEIN 60 (CBP60) protein family with a novel structural clustering algorithm

Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs (encoding 2376 unique transcripts and 1996 unique proteins) across 62 phylogenetically diverse genomes in the plant kingdom. We have employed deep learning-predicted structural analyses using AlphaFold2 and then generated dedicated web pages for all plant CBP60 proteins. Importantly, we have generated a novel clustering visualization algorithm to interrogate kingdom-wide structural similarities for more efficient inference of conserved functions across various plant taxa. Because well-characterized CBP60 proteins in Arabidopsis are known to be transcription factors with putative calmodulin-binding domains, we have integrated external bioinformatic resources to analyze protein domains and motifs. Collectively, we present a plant kingdom-wide identification of this important protein family in a user-friendly AlphaFold-anchored database, representing a novel and significant resource for the broader plant biology community.

bioinformatics↗