Adithya Polasa
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View article: Benchmarking antigen-aware inverse folding methods for antibody design
Benchmarking antigen-aware inverse folding methods for antibody design Open
Computational antibody design has seen many recent advances pioneered via the use of language models and advanced structure prediction tools. Developing a de novo antibody against a specific antigen requires structural awareness that most …
View article: nanoFOLD : sequence design of nanobodies via inverse folding
nanoFOLD : sequence design of nanobodies via inverse folding Open
Antibodies devoid of light chains are a promising class of biotherapeutics. Computational methods that address these molecules are crucially needed to accelerate the traditional, long and expensive experimental process of their discovery. …
View article: Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling
Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling Open
Protease-containing ABC transporters (PCATs) couple the energy of ATP hydrolysis to the processing and export of diverse cargo proteins across cell membranes to mediate antimicrobial resistance and quorum sensing. Here, we combine biochemi…
View article: Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase
Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase Open
YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer in bacteria. YidC facilitates the in…
View article: Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1
Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1 Open
Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor that regulates critical physiological processes including pain, appetite, and cognition. Understanding the conformational dynamics of CB1 associated with transitions between inac…
View article: Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling
Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling Open
Protease-containing ABC transporters (PCATs) couple the energy of ATP hydrolysis to the processing and export of diverse cargo proteins across cell membranes to mediate antimicrobial resistance and quorum sensing. Here, we combine biochemi…
View article: Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1
Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1 Open
Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor (GPCR) that regulates critical physiological processes including pain, appetite, and cognition. Understanding the confor- mational dynamics of CB1 associated with transitions bet…
View article: Cholesterol Dependence of the Conformational Changes in Metabotropic Glutamate Receptor 1
Cholesterol Dependence of the Conformational Changes in Metabotropic Glutamate Receptor 1 Open
Metabotropic glutamate receptors (mGluRs) are class C G protein-coupled receptors that function as obligate dimers in regulating neurotransmission and synaptic plasticity in the central nervous system. The mGluR1 subtype has been shown to …
View article: cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach
cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach Open
The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light…
View article: Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters
Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters Open
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformat…
View article: Binding affinity estimation from restrained umbrella sampling simulations
Binding affinity estimation from restrained umbrella sampling simulations Open
The protein–ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven metho…
View article: An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations
An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations Open
YidC is a membrane protein that facilitates the insertion of newly synthesized proteins into lipid membranes. Through YidC, proteins are inserted into the lipid bilayer via the SecYEG-dependent complex. Additionally, YidC functions as a ch…
View article: Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase
Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase Open
YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer, and this process is facilitated by …
View article: An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations
An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations Open
YidC is a membrane protein that facilitates the insertion of newly synthesized proteins into lipid membranes. Through YidC, proteins are inserted into the lipid bilayer via the SecYEG-dependent complex. Additionally, YidC functions as a ch…
View article: Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1
Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1 Open
Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV…
View article: Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoprotein
Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoprotein Open
View article: Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel
Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel Open
View article: Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesis
Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesis Open
Computational binding affinity estimations predict that protein-fused peptides mediate nanoparticle formation in a more controlled fashin as compared to free peptides, an observation that is also validated experimentally.
View article: Computational Elucidation of Recombinant Fusion Protein Effect on Peptide-Directed Nanoparticles
Computational Elucidation of Recombinant Fusion Protein Effect on Peptide-Directed Nanoparticles Open
Nanoparticles synthesized using various peptides have optimized properties and functional abilities which can be achieved via peptide flexibility and site specificity. Using peptide Pd4 and other alanine substitution combinations of Pd4 at…
View article: Investigation of Cyclic AMP Binding Interactions with Isolated Cyclic Nucleotide Binding Domain of HCN1 Channel using Atomistic Molecular Dynamics Simulations at Microsecond Timescale
Investigation of Cyclic AMP Binding Interactions with Isolated Cyclic Nucleotide Binding Domain of HCN1 Channel using Atomistic Molecular Dynamics Simulations at Microsecond Timescale Open
View article: Comparing the Dynamic Differences between X-ray and Cryo-EM Structures of Cannabinoid Receptor 1 using Molecular Dynamics Simulations
Comparing the Dynamic Differences between X-ray and Cryo-EM Structures of Cannabinoid Receptor 1 using Molecular Dynamics Simulations Open
View article: Developing Efficient Transfer Free Energy Calculation Methods for Hydrophobicity Predictions
Developing Efficient Transfer Free Energy Calculation Methods for Hydrophobicity Predictions Open
View article: An Investigation of the Disulfide Bridge Formation of a Thylakoid Protease using Nanosecond-Level MD Simulations
An Investigation of the Disulfide Bridge Formation of a Thylakoid Protease using Nanosecond-Level MD Simulations Open
View article: Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2
Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2 Open
The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to …
View article: An Investigation of the YidC-Mediated Membrane Insertion of a Pf3 Coat Protein Using MD Simulations
An Investigation of the YidC-Mediated Membrane Insertion of a Pf3 Coat Protein Using MD Simulations Open
View article: Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel
Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel Open
Mechanosensitive (MS) channels detect and respond to changes in the pressure profile of cellular membranes and transduce the mechanical energy into electrical and/or chemical signals. However, by re-engineering the MS channels, chemical si…
View article: Binding Free Energy Calculations of NMDA Glutamate Receptors
Binding Free Energy Calculations of NMDA Glutamate Receptors Open