P. Tao

Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations

This study uses AlphaFold2 and molecular dynamics to predict conformational ensembles and binding mechanisms of SARS-CoV-2 Omicron variants, showing agreement with experimental data.

Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling

This study adapts AlphaFold2 to predict conformational ensembles and allosteric states of ABL kinase using sequence scanning and frustration profiling, revealing limitations in detecting low-populated inactive states.

Microsecond Molecular Dynamics Simulations and Markov State Models of Mutation-Induced Allosteric Mechanisms for the Light-Oxygen-Voltage 2 Protein : Revealing Structural Basis of Signal Transmission Induced by Photoactivation of the Light Protein State

This study uses molecular dynamics simulations and Markov state models to analyze mutation-induced allostery in AsLOV2, identifying key β-sheet interactions critical for signal transmission during photoactivation.

AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance

This study uses AlphaFold2 and molecular simulations to analyze how mutations in SARS-CoV-2 Spike protein variants balance ACE2 binding and antibody resistance through epistatic interactions.

Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling

This study uses AlphaFold2 and molecular dynamics to analyze the structure, dynamics, and binding of SARS-CoV-2 Omicron BA.2.86 spike protein with ACE2 and antibodies, revealing key mutations that enhance immune evasion and ACE2 binding.

Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes

This study uses simulations and analysis of SARS-CoV-2 Omicron variants to examine conformational dynamics, protein stability, and evolution of cryptic binding pockets in the spike complex with ACE2.

Rapid Development of a Mucosal Nanoparticle Flu Vaccine by Genetic Engineering of Bacteriophage T4 using CRISPR-Cas

This study develops a mucosal nanoparticle flu vaccine using CRISPR-Cas to engineer bacteriophage T4, showing it induces both mucosal and systemic immunity in mice.

Defense mechanism of a bacterial retron supramolecular assembly

The paper identifies a phage-encoded DNA methyltransferase as a trigger for the Ec86 retron system and describes its supramolecular assembly and defense mechanism.

BacScan: An Unbiased and Genome-Wide Approach to Identify Bacterial Highly Immunogenic Proteins

BacScan identifies highly conserved immunogenic bacterial proteins across serotypes, showing potential for vaccine development.

Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms

This study uses computational methods to analyze conformational dynamics and allosteric pockets in SARS-CoV-2 Omicron variants bound to ACE2, revealing how convergent mutations influence immune escape and functional mechanisms.

Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships

This study uses simulations and profiling to analyze how Omicron mutations affect binding, allostery, and thermodynamics in SARS-CoV-2 complexes with ACE2.

Probing Conformational Landscapes and Mechanisms of Allosteric Communication in the Functional States of the ABL Kinase Domain Using Multiscale Simulations and Network-Based Mutational Profiling of Allosteric Residue Potentials

This study uses multiscale simulations and network-based mutational profiling to analyze conformational dynamics and allosteric communication in the ABL kinase domain, identifying key regulatory hotspots.

The complex roles of genomic DNA modifications of bacteriophage T4 in resistance to nuclease-based defense systems of E. coli

The paper investigates how genomic modifications in phage T4 DNA affect its resistance to nuclease-based defense systems in E. coli, revealing roles beyond simple DNA degradation prevention.

Targeted Bacteriophage T4 Nanoparticles Reverse HIV-1 Latency in CD4+ Human T Cells

The paper shows that CD4-targeted bacteriophage T4 nanoparticles reactivate HIV-1 latency in CD4+ T-cells without global activation or cytokine storm.

Bacteriophage T4 Vaccine Platform for Next-generation Influenza Vaccine Development

This study demonstrates a T4 phage-based vaccine platform that incorporates M2e antigens, showing high immunogenicity and complete protection against influenza without adjuvants.

Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago

The paper identifies potent SARS-CoV-2 neutralizing antibodies from a pre-pandemic human antibody library, showing high somatic hypermutation and specific binding to the spike protein.

Cytotoxic effects of tRNA-derived fragments and tRNA halves from non-pathogenic Escherichia coli strain on colorectal cancer cells

This study investigates the cytotoxic effects of tRNA-derived fragments and tRNA halves from non-pathogenic E. coli on colorectal cancer cells, finding that tRFs exhibit significant anticancer potential.

Cotranslational protein folding can promote the formation of correct folding intermediate

This paper uses molecular dynamics simulations to study cotranslational folding of three β-proteins, finding that it enhances helical population and reduces nonnative contacts, with one state resembling a correct folding intermediate.

Probing protein allostery as a residue-specific concept via residue perturbation maps

The paper introduces residue perturbation maps to represent allosteric effects as residue-specific properties using machine learning on molecular dynamics simulations.