Biology subjects

Swapna, G. V. T.

Publications and source records attributed to Swapna, G. V. T..

5 recordsLinked to original sources

bioRxiv2024

Modeling Alternative Conformational States of Pseudo-Symmetric Solute Carrier Transporters using Methods from Machine Learning

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/603529v3_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@15d91e0org.highwire.dtl.DTLVardef@142fc7org.highwire.dtl.DTLVardef@14ce940org.highwire.dtl.DTLVardef@6579d4_HPS_FORMAT_FIGEXP M_FIG C_FIG Conformational memorization impacts the performance of AlphaFold in modeling the dynamic structures of proteins. The Solute Carrier (SLC) superfamily of integral membrane proteins transport a wide array of small molecules across plasma and organelle membranes, and function as important drug transporters and as viral receptors. They populate different conformational states during the solute transport process, including outward-open, intermediate (occluded), and inward-open conformational states. For some SLC proteins this structural "flipping" corresponds to swapping between conformations of their N-terminal and C-terminal symmetry-related sub-structures. Conventional AlphaFold2, AlphaFold3, or Evolutionary Scale Modeling methods typically generate models for only one of these multiple conformational states of SLC proteins. While several AI-based protocols for modeling multiple conformational states of proteins have been described recently, these methods are often impacted by "memorization" of one of the alternative conformational states, and do not always provide both the inward- and outward-open conformations of SLC proteins. Here we assess the impact of memorization in modeling SLC proteins with AlphaFold, and describe a combined ESM - template-based-modeling process, based on a previously described template-based modeling method that relies on the internal pseudo-symmetry of many SLC proteins, to consistently model the alternate conformational states of SLC proteins. We also demonstrate how the resulting multi-state models can be validated experimentally by comparison with sequence-based evolutionary co-variance data (ECs) that encode information about contacts present in the various conformational states adopted by the protein. This simple, rapid, and robust approach for modeling conformational landscapes of pseudo-symmetric SLC proteins is demonstrated for several integral membrane protein transporters, including SLC35F2 the receptor of a feline leukemia virus envelope protein required for viral entry into eukaryotic cells.

bioinformatics↗

bioRxiv2022

SpecDB: A Relational Database for Archiving Biomolecular NMR Spectra Data

NMR is a valuable experimental tool in the structural biologists toolkit to elucidate the structures, functions, and motions of biomolecules. The progress of machine learning, particularly in structural biology, reveals the critical importance of large, diverse, and reliable datasets in developing new methods and understanding in structural biology and science more broadly. Protein NMR research groups produce large amounts of data, and there is renewed interest in organizing this data to train new, sophisticated machine learning architectures to improve biomolecular NMR analysis pipelines. The foundational data type in NMR is the free-induction decay (FID). There are opportunities to build sophisticated machine learning methods to tackle long-standing problems in NMR data processing, resonance assignment, dynamics analysis, and structure determination using NMR FIDs. Our goal in this study is to provide a lightweight, broadly available tool for archiving FID data as it is generated at the spectrometer, and grow a new resource of FID data and associated metadata. This study presents a relational schema for storing and organizing the metadata items that describe an NMR sample and FID data, which we call Spectra Database (SpecDB). SpecDB is implemented in SQLite and includes a Python software library providing a command-line application to create, organize, query, backup, share, and maintain the database. This set of software tools and database schema allow users to store, organize, share, and learn from NMR time domain data. SpecDB is freely available under an open source license at https://github.rpi.edu/RPIBioinformatics/SpecDB. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/480212v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@11a8109org.highwire.dtl.DTLVardef@10da6a6org.highwire.dtl.DTLVardef@137ffb5org.highwire.dtl.DTLVardef@174c5b9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Structure determination of protein-peptide complexes from NMR chemical shift data using MELD.

Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding upon binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine structures of peptide-protein complexes. Here, we demonstrate this approach for polypeptide complexes formed with the extraterminal (ET) domain of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can form different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only backbone chemical shift data, in excellent agreement with experimentally-determined structures. The approach also predicts relative binding affinities of different peptides. This hybrid MELD-NMR approach provides a powerful new tool for structural analysis of protein-polypeptide complexes in the low NMR information content regime, which can be used successfully for flexible systems where one polypeptide binding partner folds upon complex formation.

biophysics↗

bioRxiv2021

Structural Evolution of the Ancient Enzyme, Dissimilatory Sulfite Reductase

Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme accompanied diversification of sulfate/sulfite reducing organisms (SRO) into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving SRO lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.

biophysics↗

bioRxiv2020

A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

The extra-terminal (ET) domain of BRD3 is conserved among BET proteins (BRD2, BRD3, BRD4), interacting with multiple host and viral protein-protein networks. Solution NMR structures of complexes formed between BRD3-ET domain with either the 79-residue murine leukemia virus integrase (IN) C-terminal domain (IN329-408), or its 22-residue IN tail peptide (TP) (IN386-407) alone, reveal similar intermolecular three-stranded {beta}-sheet formation. 15N relaxation studies reveal a 10-residue linker region (IN379-388) tethering the SH3 domain (IN329-378) to the ET-binding motif (IN389-405)-ET complex. This linker has restricted flexibility, impacting its potential range of orientations in the IN - nucleosome complex. The complex of the ET-binding peptide of host NSD3 protein (NSD3148-184) and BRD3-ET domain includes a similar three-stranded {beta}-sheet interaction, but the orientation of the {beta}-hairpin is flipped compared to the two IN : ET complexes. These studies expand our understanding of molecular recognition polymorphism in complexes of ET-binding motifs with viral and host proteins. HighlightsO_LIThe BRD3 ET domain binds to key peptide motifs of diverse host and viral proteins. C_LIO_LIThese complexes reveal conformational plasticity in molecular recognition. C_LIO_LINMR studies demonstrate restricted interdomain motion in the IN CTD / ET complex. C_LIO_LIA cost-effective approach is described for producing isotopically-labeled peptides. C_LI Etoc BlurbWe address structurally how the MLV Integrase (IN) usurps the host function of the BET protein through comparative studies of the IN : Brd3 ET complex with that of the host NSD3. MLV integration and thus its pathogenesis is driven through protein interactions of the IN : BET family.

microbiology↗