Article
Chemistry, Physical
Junyeol Lee, Seungmin Yoon, Rakwoo Chang
Summary: In this study, the membrane structure of a typical CSL, Danicalipin A, was investigated using coarse-grained and atomistic molecular dynamics simulations. It was observed that Danicalipin A lipids form a stable monolayer membrane structure with high thermal stability.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Medicinal
Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
Summary: A new strategy for accurately predicting binding free energies of medium-sized protein-protein complexes within the microsecond timescale is introduced in this article. This strategy combines an ergodic-sampling algorithm known as Gaussian-accelerated molecular dynamics (GaMD) with a geometrical route that uses geometrical restraints to facilitate the physical separation of the binding partners. Numerical applications demonstrate the effectiveness of this strategy with low errors in binding free energy calculations for various protein-protein complexes. Compared to the classical geometrical route, this new strategy shows improved convergence properties and robustness, making it suitable for studying recognition-association phenomena in physical, biological, and medicinal chemistry.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
Summary: A new strategy for predicting binding free energies of protein-protein complexes is introduced in this article. By combining an ergodic-sampling algorithm with a geometrical route, accurate calculations can be achieved within the microsecond timescale. The strategy reduces computational cost and human effort, and has shown good convergence properties and robustness for protein-protein complexes. Numerical applications have demonstrated low errors for various protein complexes. The strategy has broad applications in physical, biological, and medicinal chemistry.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Shicheng Zhang, Ryan H. Gumpper, Xi-Ping Huang, Yongfeng Liu, Brian E. Krumm, Can Cao, Jonathan F. Fay, Bryan L. Roth
Summary: Designer receptors exclusively activated by designer drugs (DREADDs) are a chemogenetic technology used for remote control of neuronal activity. This study reports four high-resolution structures of DREADDs, revealing key details of the recognition of DREADD chemogenetic actuators and the molecular basis for activation.
Article
Multidisciplinary Sciences
Santhosh Kumar Nagarajan, Sathya Babu, Seema A. Kulkarni, Aanand Vadivelu, Panneer Devaraju, Honglae Sohn, Thirumurthy Madhavan
Summary: The study identified important residues and conformational dynamics involved in the binding of SSTR2 with ligands, suggesting potential novel drug targets with higher activity and SSTR2-selectivity. The presence of lipid molecules was found to be crucial for the formation of secondary structural domains by the extracellular regions of SSTR2, highlighting the complexities in SSTR2 functioning upon ligand binding for designing new drugs.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Medicinal
Haohao Fu, Haochuan Chen, Wensheng Cai, Xueguang Shao, Christophe Chipot
Summary: BFEE2 aims to automate and streamline accurate absolute binding free-energy estimation, eliminating the need for extensive human intervention. It supports a wide range of force fields, provides standardized workflows, and monitors the convergence of free-energy calculations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Nanoscience & Nanotechnology
Jhulan Powrel, Narayan Prasad Adhikari
Summary: Through molecular dynamics simulation, it was found that normal hemoglobin is more stable and rigid compared to sickle hemoglobin. Normal hemoglobin has a higher hydrogen bond binding force and a smaller solvent accessible surface area, while sickle hemoglobin exhibits more significant interactions in van der Waals, electrostatic, hydrophobic, and salt bridge interactions.
Article
Chemistry, Physical
Iftikhar Hussain, Tanveer Hussain, Syed Bilal Ahmed, Thanayut Kaewmaraya, Muhammad Ahmad, Xi Chen, Muhammad Sufyan Javed, Charmaine Lamiel, Kaili Zhang
Summary: Transition metal phosphides and phosphates are emerging as promising electrode materials for energy storage devices. A new trimetallic Zn-Co-Ga phosphate electrode material shows significantly higher specific capacity than mono- or bimetallic phosphates, along with superior conductivity and coulombic efficiency. Density functional theory calculations suggest that the enhanced metallic conductivity of ZCGP is due to modified exchange splitting from the 3d-orbitals of Co atoms in the presence of Zn and Ga. An engineered hybrid supercapacitor device using ZCGP//rGO demonstrates high energy and power densities, making it a potential candidate for energy storage applications.
JOURNAL OF POWER SOURCES
(2021)
Article
Chemistry, Physical
Luan Carvalho Martins, Elio A. Cino, Rafaela Salgado Ferreira
Summary: Free energy perturbation calculations are widely used in drug discovery to estimate the relative free energy of small molecules to biomolecular targets. PyAutoFEP, an open-source tool written in Python3, automates the setup of FEP calculations for improved correlation between predictions and experimental data, supporting multiple force fields and enhanced sampling methods. Results show promising potential for PyAutoFEP in lead optimization by accurately predicting molecular properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemistry & Molecular Biology
Alexander E. Aleshin, Yong Yao, Amer Iftikhar, Andrey A. Bobkov, Jinghua Yu, Gregory Cadwell, Michael G. Klein, Chuqiao Dong, Laurie A. Bankston, Robert C. Liddington, Wonpil Im, Garth Powis, Francesca M. Marassi
Summary: This study elucidates the structural basis for PLEKHA7 recognition of membrane-bound PIPs, showing that the interaction is multivalent and induces PIP clustering. The findings reveal the central role of membrane assembly in mediating protein-PIP association and provide insights into the function of the PH domain in PLEKHA7 signaling, adhesion, and nanoclustering.
Article
Chemistry, Physical
Atiyeh (Najla) Hosseini, Mikael Lund, Mohammad Reza Ejtehadi
Summary: This article introduces a correction Pair Forces method to improve the accuracy of NP-membrane translocation free energy calculations by calculating the forward and backward pulling forces for the Jarzynski free-energy estimator using steered molecular dynamics simulation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
E. Duboue-Dijon, J. Henin
Summary: The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is complex, with counter-intuitive aspects. The role of symmetry and symmetry number corrections are discussed, highlighting potential misconceptions. It is established that partial or missing sampling of symmetric bound states does not affect the calculated decoupling free energies.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yulin Jiang, Wei Zhou, Ning He, Siyang Yan, Shaoyun Chen, Jiaxu Liu
Summary: This study successfully prepared binder-free SSZ-13 zeolite and found that it exhibited excellent performance in CO2 adsorption and oxidative dehydrogenation catalysis.
Article
Multidisciplinary Sciences
Balint Dudas, David Perahia, Erika Balog
Summary: RalF, an Arf GEF from Legionella pneumophilia, is autoinhibited in its crystal structure. The mechanism of lifting this autoinhibition is unknown. Molecular Dynamics alone is not efficient to determine the active structure of RalF, but using MDeNM combined with experimental findings bridged the gap between experiments and simulation.
SCIENTIFIC REPORTS
(2021)
Article
Biophysics
Wenpeng Cao, Chuqiao Dong, Seonghan Kim, Decheng Hou, Wanbo Tai, Lanying Du, Wonpil Im, X. Frank Zhang
Summary: This study utilizes single-molecule force spectroscopy and molecular dynamics simulations to quantify the interactions between SARS-CoV-2 or SARS-CoV-1 RBD and ACE2, revealing that the N-linked glycan interaction plays a crucial role in the binding difference between the two viruses. The study uncovers the mechanism behind ACE2 binding disparity and provides insights for developing new strategies to inhibit SARS-CoV-2 entry.
BIOPHYSICAL JOURNAL
(2021)
Article
Computer Science, Interdisciplinary Applications
Sunhwan Jo, Wei Jiang
COMPUTER PHYSICS COMMUNICATIONS
(2015)
Article
Biophysics
Xi Cheng, Sunhwan Jo, Francesca M. Marassi, Wonpil Im
BIOPHYSICAL JOURNAL
(2013)
Article
Biophysics
Emilia L. Wu, Olof Engstrom, Sunhwan Jo, Danielle Stuhlsatz, Min Sun Yeom, Jeffery B. Klauda, Goran Widmalm, Wonpil Im
BIOPHYSICAL JOURNAL
(2013)
Article
Chemistry, Medicinal
Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda, Wonpil Im
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2013)
Article
Chemistry, Medicinal
Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, Wonpil Im
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2014)
Article
Chemistry, Multidisciplinary
Jong Cheol Jeong, Sunhwan Jo, Emilia L. Wu, Yifei Qi, Viviana Monje-Galvan, Min Sun Yeom, Lev Gorenstein, Feng Chen, Jeffery B. Klauda, Wonpil Im
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2014)
Article
Chemistry, Multidisciplinary
Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Davila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M. Venable, Jeffery B. Klauda, Wonpil Im
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2014)
Article
Biochemistry & Molecular Biology
Sunhwan Jo, Wonpil Im
NUCLEIC ACIDS RESEARCH
(2013)
Article
Biochemical Research Methods
Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoit Roux
PLOS COMPUTATIONAL BIOLOGY
(2014)
Article
Chemistry, Medicinal
Vincent D. Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu, Wenjuan Jiang, Alexander D. MacKerell
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Article
Chemistry, Physical
Donghyuk Suh, Sunhwan Jo, Wei Jiang, Chris Chipot, Benoit Roux
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2019)
Article
Medicine, Research & Experimental
Sunhwan Jo, Amy Xu, Joseph E. Curtis, Sandeep Somani, Alexander D. MacKerell
MOLECULAR PHARMACEUTICS
(2020)
Review
Chemistry, Multidisciplinary
Himanshu Goel, Anthony Hazel, Wenbo Yu, Sunhwan Jo, Alexander D. MacKerell
Summary: SILCS utilizes molecular simulation to obtain functional group affinity patterns for drug discovery, allowing for identification of novel ligand binding pockets, prediction of protein-ligand binding affinities, and other applications in computer-aided drug design. It represents a comprehensive approach to improve drug development processes through accuracy and throughput enhancements.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Himanshu Goel, Anthony Hazel, Vincent D. Ustach, Sunhwan Jo, Wenbo Yu, Alexander D. MacKerell
Summary: This study utilized SILCS methodology to predict protein-ligand binding affinities on eight target proteins, optimizing atomic free energy contributions using a Bayesian Markov chain Monte Carlo approach to improve prediction accuracy. The results validate the accuracy and computational efficiency of SILCS methodology for lead optimization and drug discovery.