@article {46396, title = {Structural basis of Iridoid synthase mediated cyclization of 10-oxogeranial}, journal = {Acta Crystallographica A-Foundation and Advances}, volume = {70}, year = {2014}, month = {MAY}, pages = {C270}, type = {Meeting Abstract}, keywords = {Cryo-EM, iridoid synthase, Single Particle reconstruction}, issn = {2053-2733}, author = {Sandholu, Anandsukeerthi and H. V. Thulasiram and Sengupta, Jayati and Kulkarni, Kiran} } @article {46391, title = {Structural studies on an atypical Rho GTPase RhoH}, journal = {Acta Crystallographica A-Foundation and Advances}, volume = {70}, year = {2014}, month = {MAY}, pages = {C389}, type = {Meeting Abstract}, keywords = {lymphoma, RhoH, TCR signalling}, issn = {2053-2733}, author = {Motiwala, Zenia and Kulkarni, Kiran} } @article { ISI:000362611300009, title = {Atomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain}, journal = {Journal of Molecular Biology}, volume = {427}, number = {20}, year = {2015}, month = {OCT}, pages = {3300-3315}, publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD}, address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND}, abstract = {

Many essential biological processes are mediated by complex molecular machines comprising multiple subunits. Knowledge on the architecture of individual subunits and their positions within the overall multimeric complex is key to understanding the molecular mechanisms of macromolecular assemblies. The anaphase-promoting complex/cyclosome (APC/C) is a large multisubunit complex that regulates cell cycle progression by ubiquitinating cell cycle proteins for proteolysis by the proteasome. The holo-complex is composed of 15 different proteins that assemble to generate a complex of 20 subunits. Here, we describe the crystal structures of Apc4 and the N-terminal domain of Apc5 (Apc5(N)). Apc4 comprises a WD40 domain split by a long alpha-helical domain, whereas Apc5(N) has an alpha-helical fold. In a separate study, we had fitted these atomic models to a 3.6-angstrom-resolution cryo-electron microscopy map of the APC/C. We describe how, in the context of the APC/C, regions of Apc4 disordered in the crystal assume order through contacts to Apc5, whereas Apc5(N) shows small conformational changes relative to its crystal structure. We discuss the complementary approaches of high-resolution electron microscopy and protein crystallography to the structure determination of subunits of multimeric complexes. (c) 2015 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd.

}, keywords = {anaphase-promoting complex, cell cycle, multisubunit structure, protein crystallography, ubiquitin}, issn = {0022-2836}, doi = {10.1016/j.jmb.2015.08.023}, author = {Cronin, Nora B. and Yang, Jing and Zhang, Ziguo and Kulkarni, Kiran and Chang, Leifu and Yamano, Hiroyuki and Barford, David} } @article {43525, title = {Nucleotide dependent switching in Rho GTPase: conformational heterogeneity and competing molecular interactions}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {APR}, pages = {Article Number: 45829}, abstract = {Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/ GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of "sub-states" such as state 1 \& state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound "OFF" state have very similar conformations, whereas the GTP bound "ON" state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the gamma- phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors.}, doi = {10.1038/srep45829}, author = {Kumawat, Amit and Chakrabarty, Suman and Kulkarni, Kiran} } @article {44647, title = {Dynamics of loops at the substrate entry channel determine the specificity of iridoid synthases}, journal = {Febs Letters}, volume = {592}, year = {2018}, month = {AUG}, pages = {2624-2635}, abstract = {

Iridoid synthases belong to the family of short-chain dehydrogenase reductase involved in the biosynthesis of iridoids. Despite having high sequence and structural homology with progesterone 5 beta- reductase, these enzymes exhibit differential substrate specificities. Previously, two loops. L1 and L2 at substrate-binding pocket, were suggested to be involved in generating substrate specificity. However, the structural basis of specificity determinants was elusive. Here, combining sequence and structural analysis, site-directed mutagenesis, and molecular dynamics simulations, we have shown that iridoid synthase contains two channels for substrate entry whose geometries are altered by L1-L2 dynamics, primarily orchestrated by interactions of residues Glu161 and Gly162 of L1 and Asn358 of L2. A complex interplay of these interactions confer the substrate specificity to the enzyme.

}, keywords = {iridoid synthase, iridoids, Molecular dynamics simulations, progesterone 5 beta-reductase, Substrate specificity}, issn = {1873-3468}, doi = {10.1002/1873-3468.13174}, author = {Sandholu, Anand S. and Mohole, Madhura and Duax, William L. and Thulasiram, Hirekodathakallu V. and Sengupta, Durba and Kulkarni, Kiran} } @article {46914, title = {Structural studies on 10-hydroxygeraniol dehydrogenase: a novel linear substrate-specific dehydrogenase from Catharanthus roseus}, journal = {Proteins-Structure Function and Bioinformatics}, volume = {88}, year = {2020}, month = {SEP}, pages = {1197-1206}, type = {Article}, abstract = {

Conversion of 10-hydroxygeraniol to 10-oxogeranial is a crucial step in iridoid biosynthesis. This reaction is catalyzed by a zinc-dependent alcohol dehydrogenase, 10-hydroxygeraniol dehydrogenase, belonging to the family of medium-chain dehydrogenase/reductase (MDR). Here, we report the crystal structures of a novel 10-hydroxygeraniol dehydrogenase from Catharanthus roseus in its apo and nicotinamide adenine dinucleotide phosphate (NADP(+)) bound forms. Structural analysis and docking studies reveal how subtle conformational differences of loops L1, L2, L3, and helix alpha 9{\textquoteright} at the orifice of the catalytic site confer differential activity of the enzyme toward various substrates, by modulating the binding pocket shape and volume. The present study, first of its kind, provides insights into the structural basis of substrate specificity of MDRs specific to linear substrates. Furthermore, comparison of apo and NADP(+) bound structures suggests that the enzyme adopts open and closed states to facilitate cofactor binding.

}, keywords = {10-hydroxygeraniol dehydrogenase, iridoid biosynthesis, medium-chain dehydrogenase, monoterpene indole alkaloids, reductase, X-ray crystallography}, issn = {0887-3585}, doi = {10.1002/prot.25891, Early Access Date = MAR 2020}, author = {Sandholu, Anand S. and Mujawar, Sharmila P. and Ramakrishnan, Krithika and Thulasiram, Hirekodathakallu V. and Kulkarni, Kiran} } @article {47106, title = {Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants}, journal = {Biochemical and Biophysical Research Communications}, volume = {536}, year = {2021}, month = {JAN }, pages = {107-114}, type = {Article}, abstract = {

Sesquiterpene synthases catalyse cyclisation of farnesyl pyrophosphate to produce diverse sesquiterpenes. Despite utilising the same substrate and exhibiting significant sequence and structural homology, these enzymes form different products. Previous efforts were based on identifying the effect of divergent residues present at the catalytic binding pocket on the product specificity of these enzymes. However, the rationales deduced for the product specificity from these studies were not generic enough to be applicable to other phylogenetically distant members of this family. To address this problem, we have developed a novel approach combining sequence, structural and dynamical information of plant sesquiterpene synthases (SSQs) to predict product modulating residues (PMRs). We tested this approach on the SSQs with known PMRs and also on sesquisabinene synthase 1 (SaSQS1), a SSQ from Indian sandalwood. Our results show that the dynamical sectors of SSQs obtained from molecular dynamics simulation and their hydrophobicity and vicinity indices together provide leads for the identification of PMRs. The efficacy of the technique was tested on SaSQS1 using mutagenesis. To the best of our knowledge, this is a first technique of this kind which provides cues on PMRs of SSQs, with divergent phylogenetic relationship. (C) 2020 Elsevier Inc. All rights reserved.

}, keywords = {molecular dynamics, Product specificity, Sesquiterpene synthases, Statistical coupling analysis, X-ray crystallography}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2020.12.041}, author = {Singh, Sneha and Thulasiram, V, Hirekodathakallu and Sengupta, Durba and Kulkarni, Kiran} } @article {47111, title = {Expression, purification and crystallization of Asrij, A novel scaffold transmembrane protein}, journal = {Journal of Membrane Biology}, volume = {254}, year = {2021}, month = {FEB}, pages = {65-74}, type = {Article}, abstract = {

Asrij/OCIAD1 is a scaffold transmembrane protein belonging to the Ovarian Carcinoma Immunoreactive Antigen Domain containing protein family. In Drosophila and mouse models, Asrij localizes at the endosomal and mitochondrial membrane and is shown to regulate the stemness of hematopoietic stem cells. Interaction of Asrij with ADP Ribosylation Factor 1 (Arf1) is shown to be crucial for hematopoietic niche function and prohemocyte maintenance. Here, we report the heterologous expression, standardization of detergents and purification methodologies for crystallization of Asrij/OCIAD1. To probe the activity of bacterially expressed Asrij, we developed a protein complementation assay and conclusively show that Asrij and Arf1 physically interact. Further, we find that sophorolipids improve the solubility and monodispersibility of Asrij. Hence, we propose that sophorolipids could be novel additives for stabilization of membrane proteins. To our knowledge, this is the first study detailing methodology for the production and crystallization of a heterologously expressed scaffold membrane protein and will be widely applicable to understand membrane protein structure and function. Graphic

}, keywords = {Asrij/OCIAD1, Membrane protein crystallography, sophorolipids}, issn = {0022-2631}, doi = {10.1007/s00232-020-00166-7, Early Access Date = JAN 2021}, author = {Motiwala, Zenia and Darne, Priti and Prabhune, Asmita and Inamdar, Maneesha S. and Kulkarni, Kiran} } @article {47460, title = {GPCRs that Rh oar the Guanine nucleotide exchange factors}, journal = {Small GTPases}, year = {2021}, month = {APR}, pages = {1-16}, type = {Article}, abstract = {

Cell migration, a crucial step in numerous biological processes, is tightly regulated in space and time. Cells employ Rho GTPases, primarily Rho, Rac, and Cdc42, to regulate their motility. Like other small G proteins, Rho GTPases function as biomolecular switches in regulating cell migration by operating between GDP bound {\textquoteright}OFF{\textquoteright} and GTP bound {\textquoteright}ON{\textquoteright} states. Guanine nucleotide exchange factors (GEFs) catalyse the shuttling of GTPases from OFF to ON state. G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors that are involved in many signalling phenomena including cell survival and cell migration events. In this review, we summarize signalling mechanisms, involving GPCRs, leading to the activation of RhoGEFs. GPCRs exhibit diverse GEF activation modes that include the interaction of heterotrimeric G protein subunits with different domains of GEFs, phosphorylation, protein-protein interaction, protein-lipid interaction, and/or a combination of these processes.

}, doi = {10.1080/21541248.2021.1896963}, author = {Omble, Aishwarya and Kulkarni, Kiran} } @article {47392, title = {Machine learning classifiers aid virtual screening for efficient design of mini-protein therapeutics}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {38}, year = {2021}, month = {APR }, pages = {127852}, type = {Article}, abstract = {

De novo design of mini-proteins (4-12 kDa) has recently been shown to produce new candidates for protein therapeutics. They are temperature stable molecules that bind to the drug target with high affinity for inhibiting its interactions. The development of mini-protein binders requires laboratory screening of tens of thousands of molecules for effective target binding. In this study we trained machine learning classifiers which can distinguish, with 90\% accuracy and 80\% precision, mini-protein binders from non-binding molecules designed for a particular target; this significantly reduces the number of mini protein candidates for experimental screening. Further, on the basis of our results we propose a multi-stage protocol where a small dataset (few hundred experimentally verified target-specific mini-proteins) can be used to train classifiers for improving the efficiency of mini-protein design for any specific target.

}, keywords = {Drug design, machine learning, Mini-proteins, Protein therapeutics, virtual screening}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2021.127852}, author = {Gaur, Neeraj K. and Goyal, Venuka Durani and Kulkarni, Kiran and Makde, Ravindra D.} } @article {47354, title = {Molecular interplay at the membrane and impact on cellular physiology}, journal = {Journal of Membrane Biology}, volume = {254}, year = {2021}, month = {JUN}, pages = {239-242}, type = {Editorial Material}, issn = {0022-2631}, doi = {10.1007/s00232-021-00183-0, Early Access Date = MAY 2021}, author = {Pucadyil, Thomas and Kulkarni, Kiran and Sengupta, Durba} } @article {48043, title = {Substrate induced dynamical remodeling of the binding pocket generates GTPase specificity in DOCK family of guanine nucleotide exchange factors}, journal = {Biochemical and Biophysical Research Communications}, volume = {631}, year = {2022}, month = {NOV}, pages = {32-40}, type = {Article}, abstract = {

Dedicator of cytokinesis (DOCK) family of guanine nucleotide exchange factors (GEFs) activate two members of Rho family GTPases, Rac1/Cdc42, to exert diverse cellular processes, including cell migration. As DOCK GEFs have been critically implicated in tumour cell migration, understanding their function and specificity is imperative for designing anti-metastatic drugs. Based on their GTPase specificity they have been classified as Rac, Cdc42 and dual specific GEFs. Despite extensive structural studies, the factors that determine GTPase specificity of DOCK GEFs have remained elusive. Here, we show that subtle dynamical coupling between GEF and GTPase structures modulate the binding interface to generate mutual spec-ificity. To cluster the dynamically coupled residues in GEF-GTPase complexes a novel intra-residue backbone-torsion-angles based mutual information (TMI) technique was employed. TMI was calcu-lated from 4500 trajectories obtained from a total of 4.5ms molecular dynamics simulations performed on members of all the three clades of DOCK GEFs. The obtained clusters suggest a specificity generation mechanism that involves optimization of the binding pocket for the crucial divergent residue at the 56th position of Rac/Cdc42 (FCdc42/WRac1). These clusters encompass five residues from the structural segment lobe C -a10 helix of the DOCK proteins and functional SWI region of GTPase, which induce orchestrated structural modulations to generate the specificity. Even the conserved residues from SWI region are seen to augment the specificity defining dynamical rearrangements. Furthermore, the pro-posed dynamical GTPase-DOCK GEF specificity model was verified using mutagenesis studies on Rac1 and dual GTPase specific Dock2 and Dock6, respectively. Thus the current study provides the generic substrate specificity determinants of DOCK GEFs, which are not apparent from the conventional struc-tural analysis.(c) 2022 Elsevier Inc. All rights reserved.

}, keywords = {Dedicator of cytokinesis, GTPase specificity, Guanine exchange factors, Molecular dynamics simulations, Mutual information, Rho GTPases}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2022.09.059}, author = {Roy, Debopriya and Sengupta, Durba and Kulkarni, Kiran} } @article {48812, title = {Cocrystallization of multi-kinase inhibitor pazopanib with fenamic acids: improving dissolution and inhibiting cell migration}, journal = {CrystEngComm}, volume = {25}, year = {2023}, month = {OCT }, pages = {5565-5574}, type = {Article}, abstract = {

A multi-kinase inhibitor, pazopanib (PAZ) is cocrystallized with cyclooxygenase (COX) inhibitor fenamic acids to investigate the dissolution rate and inhibition of cell migration in VEGF-triggered HUVEC cells to test the efficacy of stoichiometric drug-drug combinations. Crystallization experiments at the sub-milligram level in an acetonitrile-methanol mixture yielded two drug-drug salt forms of PAZ with flufenamic acid (FFA) and niflumic acid (NFA) as PAZ+center dot FFA-center dot ACN (an acetonitrile solvate named as form I) and PAZ+center dot NFA-. Structures of the crystal forms were characterized by single crystal X-ray diffraction (SC-XRD) method. Crystal structures revealed that the presence of a 2-aminopyrimidine group in PAZ is a strong partner for the carboxyl group in all solid forms, forming an acidMIDLINE HORIZONTAL ELLIPSISpyrimidine heterosynthon with COX inhibitor fenamic acids. To perform dissolution experiments and cell line analysis, the scale-up of both salt forms were done in the acetonitrile-methanol mixture through crystallization, which showed a polymorphic transformation in the case of PAZ+center dot FFA-center dot ACN (an acetonitrile solvate named form II). The thermodynamic stability of PAZ+center dot FFA-center dot ACN (form II) and PAZ+center dot NFA- were analysed using slurry experiment under ambient conditions in pH 1.2 (0.1 N HCl) buffer medium and the residual solid phase was characterized by powder XRD, which showed that PAZ+center dot FFA-center dot ACN (form II) was a metastable solid form while PAZ+center dot NFA- was a stable solid form. The dissolution experiments at gastric pH 1.2 showed that the rate of dissolution of PAZ+center dot FFA-center dot ACN was 10 times higher than PAZ+center dot NFA-. The cell migration assay suggested that PAZ+center dot FFA-center dot ACN inhibited similar to 25\% and PAZ+center dot NFA- inhibited similar to 20\% migration of HUVEC cells compared to PAZ alone. These investigations suggested that the drug-drug salts PAZ+center dot FFA- and PAZ+center dot NFA- would be potential combo drug candidates for clinical trials. Multi-drug crystalline salts of pazopanib with fenamic acids exhibit enhanced dissolution and 20\% higher inhibition in the migration of HUVEC cells compared to the reference drug.

}, doi = {10.1039/d3ce00773a}, author = {Rai, Sunil K. and Gunnam, Anilkumar and Roy, Debopriya and Rajput, Raveena and Kulkarni, Kiran and Nangia, Ashwini K.} } @article {48680, title = {In silico identification and characterization of the SNPs in the human ASTL gene and their probable role in female infertility}, journal = {Frontiers in Cell and Developmental Biology}, volume = {11}, year = {2023}, month = {JUN}, pages = {1151672}, type = {Article}, abstract = {

Ovastacin (ASTL), a zinc metalloprotease, is released from a fertilized egg during exocytosis of cortical granules which occurs minutes after the sperm and egg fuse. ASTL cleaves ZP2, one of the four primary glycoproteins of human zona pellucida, and this cleavage prevents polyspermy, causes zona pellucida hardening, and also protects the pre-implantation embryo. Any perturbation in the activity of ASTL can thus disturb this process and may lead to infertility without changing the gross morphology of the oocyte. A small amount of ASTL is also released by unfertilized oocytes but its catalytic activity is absent as it is bound by its inhibitor, Fetuin-B (FETUB). Pre-mature release of ASTL when FETUB is absent also causes infertility. To identify and understand the structural and functional effects of deleterious SNPs of ASTL on its interaction with ZP2 and FETUB and hence on fertility, a total of 4,748 SNPs from the dbSNP database were evaluated using a variety of in silico tools. All of the 40 shortlisted nsSNPs were present in the catalytic domain of the protein. Comparison of the wild type with mutants using MutPred2 suggests an alteration in the catalytic activity/zinc binding site in many SNPs. Docking studies show the involvement of hydrophobic interactions and H bonding between ASTL and ZP2 and also between ASTL and FETUB. Four positions in ASTL involved in the hydrophobic interactions (P-105 and D-200 between ASTL and ZP2; D-198 and L-278 etween ASTL and FETUB) and 5 in H bonding (E-75 and R-159 between ASTL and ZP2; and K-93, R-159, and C-281 between ASTL and FETUB) have SNP{\textquoteright}s associated with them validating their importance. Interestingly, a cluster of multiple SNPs was found in the motif (DRD200)-D-198, which is also a well-conserved region among several species. Statistical Coupling Analysis (SCA) suggested that the deleterious SNPs were present in the functionally important amino acid positions of ASTL and are evolutionarily coupled. Thus, these results attempt to identify the regions in ASTL, mutations in which can affect its binding with ZP2 or FETUB and cause female infertility.

}, keywords = {ASTL, female infertility, fertilization, omics, ovastacin, single nucleotide polymorphism}, issn = {2296-634X}, doi = {10.3389/fcell.2023.1151672}, author = {Suri, Kapali and Rajput, Neha and Sharma, Priya and Omble, Aishwarya D. and Kulkarni, Kiran and Gahlay, Gagandeep K.} } @article {48673, title = {Wavelet coherence phase analysis decodes the universal switching mechanism of Ras GTPase superfamily}, journal = {iScience}, volume = {26}, year = {2023}, month = {JUL}, pages = {107031}, type = {Article}, abstract = {

The Ras superfamily of GTPases regulate critical cellular processes by shuttling between GTP-bound ON and GDP-bound OFF states. This switching mechanism is attributed to the conformational changes in two loops, SWI and SWII, upon GTP binding and hydrolysis. Since these conformational changes vary across the Ras superfamily, there is no generic parameter to define their functional states. A unique wavelet coherence (WC) analysis-based approach developed here shows that the structural changes in switch regions could be mapped onto the wavelet coherence phase couplings (WPCs). Thus, WPCs could serve as unique parameters to define their functional states. Disentanglement of WPCs in oncogenic GTPases shows how breakdown of structural allostery leads to their aberrant function. These observations stand out even for simulated ensemble of switch region conformers. Overall, for the first time, we show that WPCs could unravel the latent structural deviations in Ras proteins to decode their universal switching mechanism.

}, doi = {10.1016/j.isci.2023.107031}, author = {Motiwala, Zenia and Sandholu, Anand S. and Sengupta, Durba and Kulkarni, Kiran} }