Article
Chemistry, Physical
Sehr Naseem-Khan, Louis Lagardere, Christophe Narth, G. Andres Cisneros, Pengyu Ren, Nohad Gresh, Jean-Philip Piquemal
Summary: In this paper, the extension of the SIBFA many-body polarizable force field to condensed-phase molecular dynamics simulations is presented, showcasing its ability to reproduce energy contributions from ab initio calculations and properties in the condensed phase.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Hesam Arabzadeh, Chengwen Liu, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas Albrecht-Schonzart
Summary: In this work, the hydration of Sm2+ and Eu2+ cations were studied using AMOEBA force fields. The coordination numbers obtained were in good agreement with experimental results, and the decrease in coordination number of Ln(2+) compared with Ln(3+) was attributed to progressive water exchange events. The effects of chloride counter anions on the coordination of Ln(2+) cations were also investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Brandon Walker, Chengwen Liu, Elizabeth Wait, Pengyu Ren
Summary: A next-generation protocol (Poltype 2) has been developed to automatically generate AMOEBA polarizable force field parameters for small molecules, with significant improvements in both features and computational efficiency. The protocol shows great potential for applications, particularly in predicting binding free energy in computational drug discovery.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Nicole A. Perry-Hauser, Tamer S. Kaoud, Henriette Stoy, Xuanzhi Zhan, Qiuyan Chen, Kevin N. Dalby, Tina M. Iverson, Vsevolod V. Gurevich, Eugenia Gurevich
Summary: Arrestins were initially identified as suppressors of G protein-mediated signaling, but they are also involved in initiating various signaling pathways, including the mitogen-activated protein kinase cascades. By studying peptide fragments derived from arrestin-3, a 16-residue peptide capable of activating JNK3 was identified, which provides a valuable tool for studying neuronal apoptosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Yu-Chun Lin, Pengyu Ren, Lauren J. Webb
Summary: This study evaluates the accuracy of predicting electric fields in proteins through experiments and molecular dynamics simulations. The results demonstrate that specific simulation and truncation methods can improve the accuracy of pKa predictions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Zhifeng Jing, Pengyu Ren
Summary: This article presents molecular dynamics simulations of two protein-RNA complexes using the AMOEBA polarizable force field. The refined parameters of the force field successfully reproduced accurate quantum-mechanical data of base-base and base-amino acid interactions, resulting in a more stable hydrogen-bond network at the interface. These simulations demonstrated the potential of polarizable force fields for studying protein-RNA complexes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Xudong Yang, Chengwen Liu, Yu-An Kuo, Hsin-Chih Yeh, Pengyu Ren
Summary: “Fluorescent light-up aptamers (FLAPs) are biosensors used for cellular imaging and detecting various targets. Computational simulations using a polarizable force field have provided valuable insights into the binding mechanisms of FLAPs and the design of new aptamers or fluorogens with improved performance.”
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Medicinal
Yazdan Maghsoud, Erik Antonio Vazquez-Montelongo, Yang Xudong, Liu Chengwen, Jing Zhifeng, Juhoon Lee, Matthew Harger, Ally K. Smith, Miguel Espinoza, Guo Hou-Fu, Jonathan M. Kurie, Kevin N. Dalby, Ren Pengyu, G. Andres Cisneros
Summary: Lysyl hydroxylase-2 (LH2) catalyzes the hydroxylation of lysine to hydroxylysine. High levels of LH2 can lead to the accumulation of collagen crosslinks, causing fibrosis and specific types of cancer metastasis. Computational simulations have identified potential small molecules as inhibitors for LH2, providing insights for further design and development.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Hesam Arabzadeh, Brandon Walker, Joseph M. Sperling, Orlando Acevedo, Pengyu Ren, Wei Yang, Thomas E. Albrecht-Schonzart
Summary: To efficiently separate lanthanide elements, researchers have used molecular dynamics simulations to study the coordination of DCH18C6 with several lanthanide and actinide elements. It was found that Dy2+ and Yb2+, which have comparatively smaller ionic radii, may not be an ideal fit with DCH18C6's ring size. Additionally, the binding free energies of different DCH18C6 diastereoisomers with lanthanide elements showed variations.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Susan B. Rempe, Pengyu Ren, Elizabeth E. Wait, Justin Gourary, Chengwen Liu, Erik D. Spoerke
Summary: Rare-earth metals (REMs) are essential for various industries and medical applications. A new approach inspired by proteins' binding properties shows promise for REM refinement. Understanding the biological recognition mechanisms is crucial for the success of this bioinspired method.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Yanxing Wang, Brandon Duane Walker, Chengwen Liu, Pengyu Ren
Summary: Accurate conformational energetics are crucial for understanding chemical properties and parameterizing force fields. Traditional density functional theory (DFT) methods are time-consuming, especially for larger molecules or a large number of molecules. In this study, alternative methods including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x were compared. It was found that a sequential protocol combining geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can significantly save computational time while maintaining satisfactory energy profiles.
Article
Chemistry, Physical
Yu-Chun Lin, Pengyu Ren, Lauren J. Webb
Summary: Precisely quantifying the magnitude and direction of electric fields in proteins has been a challenge in understanding biological functions. This study compared the extent of hydrogen bonding calculated in two force fields, Amber03 and AMOEBA, at different locations in a protein and correlated it with the experimental nitrile absorption frequency. The results showed that the AMOEBA force field accurately predicted the hydrogen bonding and interactions with nearby water molecules, while the Amber03 force field had less reliable predictions. This finding is significant for accurately predicting electric fields in complex biomolecular environments.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Rae A. Corrigan, Andrew C. Thiel, Jack R. Lynn, Thomas L. Casavant, Pengyu Ren, Jay W. Ponder, Michael J. Schnieders
Summary: Computational simulation of biomolecules is important for protein design, protein-ligand binding interactions, and biomolecular folding. Implicit solvent models are attractive alternatives to explicit solvation for describing solvation effects without including solvent degrees of freedom. This study extends the parameterization of the generalized Kirkwood implicit solvent model for biomolecules and achieves accurate simulations of protein structures.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Medicinal
Juhoon Lee, Hou-fu Guo, Shike Wang, Yazdan Maghsoud, Erik Antonio Vazquez-Montelongo, Zhifeng Jing, Rae M. Sammons, Eun Jeong Cho, Pengyu Ren, G. Andres Cisneros, Jonathan M. Kurie, Kevin N. Dalby
Summary: Lysyl hydroxylase 2 (LH2) plays a crucial role in promoting lung cancer metastasis by modulating specific types of collagen cross-links within the tumor stroma. Compounds 12 and 13 demonstrate selective inhibition of LH2 activity and reduce cell migration potential.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Xudong Yang, Chengwen Liu, Pengyu Ren
Summary: This study develops quantum mechanics-based chemical bond interaction parameters, taking into account vibrational anharmonicity, coupling effects, and out-of-plane bending of hybridized atoms. The results show that this model accurately describes the vibrational properties and structures of molecules, and is more accurate than traditional harmonic models.
JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY
(2022)