Biology subjects

Kumar R., P.

Publications and source records attributed to Kumar R., P..

3 recordsLinked to original sources

bioRxiv2026

An engineered disulfide staple restricts lid loop dynamics and alters substrate specificity of phenylalanine ammonia-lyase

In Anabaena variabilis (Trichormus variabilis) phenylalanine ammonia-lyase (AvPAL), a conserved lid-like loop sits over the active site and has been studied both for its role in positioning a catalytic tyrosine and for its contribution to phenylalanine aminomutase (PAM) activity. While the active site architecture and substrate specificity of AvPAL have been extensively characterized, the dynamic behavior of this unstructured loop beyond its role in catalysis remains poorly understood. Here, we investigate the functional role of this loop by restricting its mobility through targeted interchain disulfide bond engineering. Three in-house approaches were designed to predict ideal cysteine residue pairs: (i) quantifying pair interaction energies via electrostatic and van der Waals forces, (ii) generating a contact map of residues within 5 [A] proximity, and (iii) implementing a machine-learning model trained on datasets from PDBCYS, SPX, and an internal database to rank cysteine pair likelihood within disulfide bond geometric constraints. Our machine-learning-guided strategy yielded a successful variant with complete oxidation efficiency in E. coli. Rigidification of this loop reveals that it also functions as a regulator of substrate specificity. Multi-scale molecular simulation analyses (molecular dynamics, metadynamics, quantum/molecular mechanics) reveal that this modification alters the active-site pocket by reducing the conformational dynamics of substrate binding. Our findings underscore the delicate balance between enzyme flexibility and catalytic efficiency, providing novel insights into the role of this understudied dynamic loop region in AvPAL.

bioengineering↗

bioRxiv2025

A Novel Phosphatase Reverses the Leloir Pathway to Promote Tagatose Synthesis from Glucose

D-Tagatose is a natural, low-calorie, rare monosaccharide that has gained substantial interest as an alternative sweetener. It offers numerous benefits, including a low glycemic index, prebiotic properties, and the ability to lower blood sugar levels. Currently, tagatose is primarily produced industrially through the isomerization of galactose, utilizing both chemical and enzymatic catalysis. While these established processes can produce tagatose, they are inefficient and expensive. Recent works have demonstrated alternative biosynthetic routes to produce D-tagatose but suffer from low theoretical yield and/or reliance on expensive feedstocks. This study demonstrates a novel biochemical pathway to produce D-tagatose directly from glucose using a whole-cell process with Escherichia coli. This process is distinct from other biosynthetic schemes and utilizes a newly discovered galactose-1-phosphate-selective phosphatase to drive the native Leloir pathway in reverse and synthesize the substrate D-galactose directly from D-glucose. Our analysis of the phosphatase reveals how an ensemble of intermolecular hydrogen bonds governs substrate specificity. By co-expressing this phosphatase and an L-arabinose isomerase in a modified strain background, we demonstrate production of tagatose directly from glucose. In initial studies, we generated [~]10.5 g/L galactose from 30 g/L glucose (35 % yield) while also producing > 1 g/L tagatose. This demonstrates the feasibility of a novel approach to tagatose production in vivo with a theoretical pathway yield of 94.9 %, which is substantially higher than previously proposed tagatose biosynthetic schemes.

bioengineering↗

bioRxiv2021

In-depth sequence-function characterization reveals multiple paths to enhance phenylalanine ammonia-lyase (PAL) activity.

Phenylalanine ammonia-lyases (PALs) deaminate L-phenylalanine to trans-cinnamic acid and ammonium and have idespread application in chemo-enzymatic synthesis, agriculture, and medicine. In particular, the PAL from Anabaena variabilis (Trichormus variabilis) has garnered significant attention as the active ingredient in Pegvaliase(R), the only FDA-approved drug treating classical phenylketonuria (PKU). Although an extensive body of literature exists on structure, substrate-specificity, and catalytic mechanism, protein-wide sequence determinants of function remain unknown, which limits the ability to rationally engineer these enzymes. Previously, we developed a high-throughput screen (HTS) for PAL, and here, we leverage it to create a detailed sequence-function landscape of PAL by performing deep mutational scanning (DMS). Our method revealed 79 hotspots that affected a positive change in enzyme fitness, many of which have not been reported previously. Using fitness values and structure-function analysis, we picked a subset of residues for comprehensive single- and multi-site saturation mutagenesis to improve the catalytic activity of PAL and identified combinations of mutations that led to improvement in reaction kinetics in cell-free and cellular contexts. To understand the mechanistic role of the most beneficial mutations, we performed QM/MM and MD and observed that different mutants confer improved catalytic activity via different mechanisms, including stabilizing first transition and intermediate states and improving substrate diffusion into the active site, and decreased product inhibition. Thus, this work provides a comprehensive sequence-function relationship for PAL, identifies positions that improve PAL activity when mutated and assesses their mechanisms of action.

bioengineering↗