Article
Chemistry, Physical
Qiang Sun, Weiqi Wang, Shuai Cui
Summary: Recent studies on hydrophobic interactions have shown that these interactions have a directional nature, depending on the relative orientation of solutes when they aggregate in water. The research demonstrated that as solutes approach each other, the interactions between them become stronger, and proposed a model driven by hydrophobic interactions to understand specificity and affinity of molecular recognition in water.
Article
Engineering, Industrial
Junjun Zheng, Hiroyuki Okamura, Tadashi Dohi
Summary: This paper focuses on age replacement problems under the assumption of a stochastic point process for the arrival of opportunities. By extending existing models, the relationship between replacement opportunities and arrival processes is considered, leading to a comprehensive evaluation of opportunity-based age replacement policies in a generalized modeling framework.
RELIABILITY ENGINEERING & SYSTEM SAFETY
(2021)
Article
Quantum Science & Technology
G. A. L. White, F. A. Pollock, L. C. L. Hollenberg, K. Modi, C. D. Hill
Summary: Characterization protocols have been crucial in developing noisy intermediate-scale quantum computers. This article introduces a generalized quantum process tomography method, called process tensor tomography, which can accurately describe non-Markovian dynamics. The article details the experimental requirements, necessary postprocessing algorithms, and best practices for accurate results.
Article
Agriculture, Multidisciplinary
Yuchen Bai, Hui Jiang, Yingjie Zhang, Leina Dou, Minggang Liu, Wenbo Yu, Kai Wen, Jianzhong Shen, Yuebin Ke, Xuezhi Yu, Zhanhui Wang
Summary: The study discovered the potential of newly designed small molecule haptens (hapten1-4) in enhancing antibody affinity and accuracy in recognizing capsaicinoids (CPCs), primarily through exposure of hydrophobic moieties.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Thermodynamics
Mohammadali Ahmadi, Zhangxin Chen
Summary: This paper investigates the unclear mechanisms contributing to bitumen recovery under a steam-anionic surfactant co-injection process through molecular dynamics simulation. The simulation results reveal that sulfur on resin molecules can negatively affect the oil detachment process from a quartz surface. Increasing the pumping force can improve the oil detachment process when the resin contains sulfur.
Article
Physics, Multidisciplinary
Lijuan Sun, Yu Cao, Xiaojie Chen, Qing Liang
Summary: The interactions between nanoparticles coated with hydrophilic and hydrophobic ligands and a lipid bilayer were studied using coarse-grained molecular dynamics simulation. The effects of ligand density, ratio of hydrophilic to hydrophobic ligands, and ligand rigidity on the interactions were investigated. The results showed that nanoparticles can either be inserted into or adsorbed on the lipid bilayer depending on their size, ligand ratio, and ligand flexibility. This study provides insights into modulating interactions between amphiphilic nanoparticles and lipid bilayers, and their applications in drug delivery and cell imaging.
COMMUNICATIONS IN THEORETICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Xuan Huang, Xiaoping Wang, Mao Quan, Huan Yao, Hua Ke, Wei Jiang
Summary: By designing and synthesizing endo-functionalized macrocyclic hosts with buried salt bridges, selective recognition of specific compounds can be achieved in water, which can be used for optical chirality sensing and fluorescent sensing. This demonstrates the effective use of buried salt bridges in molecular recognition in water.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Chaoying Ding, Christopher Gerberich, Marianthi Ierapetritou
Summary: Hydrophobic Interaction Chromatography (HIC) is widely used in the biopharmaceutical industry for the purification of therapeutic proteins. In this study, a hybrid model combining a multi-component Langmuir isotherm and a neural network is developed to accurately describe the complex HIC behavior. The structure of the hybrid model is found to be critical in improving accuracy. The developed model shows significant improvement in calibration and validation compared to the mechanistic model. Process optimization is also performed using the hybrid model.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Physical
Beata Korchowiec, Monika Orlof-Naturalna, Jacek Korchowiec, Jean-Bernard Regnouf de Vains, Maxime Mourer, Ewa Rogalska
Summary: The calixarene derivative tetra-p-guanidinoethylcalix[4]arene exhibited in vitro activity against various Gram-positive and Gram-negative bacteria. The study investigated the interaction between bacterial cell membranes and the water-soluble calixarene using model lipids as monomolecular films. The structure of phosphatidylglycerols influenced the affinity of the calixarene for the monolayer, suggesting potential for developing new antibiotics.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Pharmacology & Pharmacy
Yujiang Dou, Haibo Chen, Yuke Ge, Kai Yang, Bing Yuan
Summary: This study investigates the interaction between membrane-active peptides and cell membranes, showing the existence of multiple mechanisms influenced by the spatial heterogeneity of peptide distribution. The results provide support for modulating the membrane activity of peptides by adjusting their hydrophobicity and local concentration.
Article
Food Science & Technology
Xiangru Wei, Frank Monahan, Chunjiang Zhang, Zhenyu Wang, Dequan Zhang
Summary: This study analyzed the structural and functional changes of Beijing duck breast myosin during thermal treatments. Results showed that myosin denatured and unfolded at 50-55 degrees C, leading to the exposure of hydrophobic groups. The increase of hydrophobic interaction promoted myosin aggregation.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lorenzo Di Rienzo, Michele Monti, Edoardo Milanetti, Mattia Miotto, Alberto Boffi, Gian Gaetano Tartaglia, Giancarlo Ruocco
Summary: Since the outbreak of the Covid19 pandemic, efforts have been made to identify strategies to inhibit SARS-CoV-2 replication within host cells. One promising approach involves utilizing a mutant of human receptor ACE2 as a decoy to compete with endogenous ACE2 for binding to the Spike protein of SARS-CoV-2, reducing the virus' ability to enter host cells. By using a computational framework based on the 2D Zernike formalism, this study investigates molecular binding details and evaluates changes in ACE2-Spike compatibility, leading to the identification of a set of ACE2 mutants with increased shape complementarity with Spike.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Quantum Science & Technology
Philip Taranto, Felix A. Pollock, Kavan Modi
Summary: This study introduces a finite memory ansatz that approximates or recovers the true process while ensuring errors are bounded by the strength of the non-Markovian memory. The introduced memory strength is dependent on the probing method, with the recovery error constrained by the smallest memory strength across all possible methods. This allows for an unambiguous and efficient description of non-Markovian phenomena, with implications for compression and recovery techniques essential for near-term technologies.
NPJ QUANTUM INFORMATION
(2021)
Article
Engineering, Chemical
Bo Hao, Minqiang Fan
Summary: Particle-bubble attachment is crucial in coal and mineral flotation processes. In this study, the attachment process of low-rank coal particles to the bubble surface was simulated, revealing the important role of water film rupture in particle attachment.
MINERALS ENGINEERING
(2024)
Article
Computer Science, Artificial Intelligence
Lifei Chen, Haiyan Wu, Wenxuan Kang, Shengrui Wang
Summary: This paper proposes a method to represent each symbolic sequence by optimizing the transition probability distribution of a Hidden Markov Model, addressing the challenge of learning structural features within sequences in small sample size cases.
PATTERN RECOGNITION
(2022)
Article
Chemistry, Physical
Zirui Zhang, Clarisse G. Ricci, Chao Fan, Li-Tien Cheng, Bo Li, J. Andrew McCammon
Summary: The hybrid approach combines the Monte Carlo method, a variational implicit-solvent model (VISM), and a binary level-set method for simulating biomolecular binding in an aqueous solvent. It estimates the solvation free energy for the biomolecular complex by minimizing the VISM free-energy functional, accurately predicting the electrostatic part of the solvation free energy by shifting the dielectric boundary. The new and fast binary level-set method allows for this functional minimization in each MC move.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Medicinal
Terra Sztain, Rommie Amaro, J. Andrew McCammon
Summary: By using Gaussian accelerated molecular dynamics, this study identified cryptic pockets within the SARS-CoV-2 main protease, revealing druggable conformational states far from the active site. The simulations demonstrated comparable dynamics and pocket volumes to conventional brute force simulations conducted on significantly longer timescales.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Hamidreza Rahmani, Wen Ma, Zhongjun Hu, Nadia Daneshparvar, Dianne W. Taylor, J. Andrew McCammon, Thomas C. Irving, Robert J. Edwards, Kenneth A. Taylor
Summary: The atomic structure of myosin tail in thick filaments isolated from Lethocerus indicus flight muscle is asymmetric, with differences in skip regions and nonhelical C termini. The study provides insights into the uncoiling of coiled-coils at the head-tail junction and sheds light on the complex roles of thick filaments in muscle contraction across species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Terra Sztain, Thomas G. Bartholow, D. John Lee, Lorenzo Casalino, Andrew Mitchell, Megan A. Young, Jianing Wang, J. Andrew McCammon, Michael D. Burkart
Summary: Enzymes in metabolic pathways utilize a variety of regulatory mechanisms to maintain homeostasis, with carrier proteins playing an essential role in substrate shuttling. A unique communication mechanism between ACP and partner enzymes has been demonstrated, showing allosteric regulation dependent on fatty acid chain length. These findings provide insights into cargo communication by ACP and can potentially be used for engineering carrier protein-dependent pathways for specific products.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Surl-Hee Ahn, Sanbo Qin, Jason Z. Zhang, J. Andrew McCammon, Jin Zhang, Huan-Xiang Zhou
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Evan Seitz, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, Rommie E. Amaro
Summary: Through simulations, the study reveals the mechanism of spike protein receptor binding domain (RBD) opening in SARS-CoV-2 infection, highlighting the crucial role of N-glycan in facilitating RBD opening. This research represents a milestone in ensemble pathway simulations and provides a foundation for understanding the fundamental mechanisms of viral entry and infection.
Article
Multidisciplinary Sciences
Varnavas D. Mouchlis, Daiki Hayashi, Alexis M. Vasquez, Jian Cao, J. Andrew McCammon, Edward A. Dennis
Summary: Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)) associates with lipoproteins in human plasma and hydrolyzes oxidized phospholipids. The mechanism of enzyme-membrane association and substrate specificity were studied using lipidomics and mass spectrometry techniques.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Thomas G. Laughlin, Amar Deep, Amy M. Prichard, Christian Seitz, Yajie Gu, Eray Enustun, Sergey Suslov, Kanika Khanna, Erica A. Birkholz, Emily Armbruster, J. Andrew McCammon, Rommie E. Amaro, Joe Pogliano, Kevin D. Corbett, Elizabeth Villa
Summary: This study identifies a protein called ChmA as the main component of the bacteriophage nuclear shell. The structure and dynamics of the ChmA shell provide insights into its formation and functions.
Article
Biochemistry & Molecular Biology
Surl-Hee Ahn, Gary A. Huber, J. Andrew McCammon
Summary: Intrinsically disordered proteins (IDPs) have attracted significant attention due to their involvement in biological processes and diseases. Computational studies using Brownian dynamics (BD) simulations with a coarse-grained force field for proteins (COFFDROP) have been conducted to complement experimental work. The researchers found that IDPs' properties, such as hydrodynamic radii and entanglement indices, are influenced by salt concentration.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Joshua C. Corpuz, Ashay Patel, Tony D. Davis, Larissa M. Podust, J. Andrew McCammon, Michael D. Burkart
Summary: This study reveals the binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains in non-ribosomal peptide synthetases (NRPSs) using chemical biology approaches. The research also demonstrates the possibility of controlling PCP binding specificity through modifying interfacial interactions.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yohei Takahashi, Krystal C. Bosmans, Po -Kai Hsu, Karnelia Paul, Christian Seitz, Chung-Yueh Yeh, Yuh-Shuh Wang, Dmitry Yarmolinsky, Maija Sierla, Triin Vahisalu, J. Andrew McCammon, Jaakko Kangasjaervi, Li Zhang, Hannes Kollist, Thien Trac, Julian I. Schroeder
Summary: The rise in atmospheric CO2 concentration affects stomatal closing in plants, impacting transpirational water loss, photosynthesis, and growth. This study identifies MPK4/12 and HT1 as the primary CO2 sensors in plants, located upstream of the CBC1 kinase. These findings are significant for understanding the plant response to CO2.
Article
Biochemistry & Molecular Biology
Jui-Hung Weng, Wen Ma, Jian Wu, Pallavi Kaila Sharma, Steve Silletti, J. Andrew McCammon, Susan Taylor
Summary: Mutations in LRRK2 increase the risk of Parkinson's disease, and its pathological functions are often associated with abnormal kinase activity. This study combines enhanced sampling simulations with HDX-MS to investigate the dynamic changes and allosteric communications within the C-terminal domains of LRRK2. It is found that different types of kinase inhibitors stabilize distinct kinase conformations and modulate the interdomain interactions between the kinase and GTPase domains.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Terra Sztain, Joshua C. Corpuz, Thomas G. Bartholow, Javier O. Sanlley Hernandez, Ziran Jiang, Desirae A. Mellor, Graham W. Heberlig, James J. La Clair, J. Andrew Mccammon, Michael D. Burkart
Summary: Carrier-protein-dependent metabolic pathways rely on protein-protein interactions to control enzyme reactivity and timing. Computational methods, such as the improved Rosetta score function, can be used to design customized pathways by optimizing protein-protein interactions. This method provides a promising platform for engineering carrier-protein-dependent pathways.
ACS CHEMICAL BIOLOGY
(2023)
Article
Physics, Applied
Marcus T. Hock, Abigail E. Teitgen, Kimberly J. McCabe, Sophia P. Hirakis, Gary A. Huber, Michael Regnier, Rommie E. Amaro, J. Andrew McCammon, Andrew D. McCulloch
Summary: dATP, a natural analog of ATP, has been shown to enhance cardiac function. In this study, computational modeling was used to investigate the mechanism by which dATP accelerates calcium re-uptake into the sarcoplasmic reticulum during cardiac relaxation. The results showed that dATP interacts with SERCA and increases calcium association rate constants, ultimately leading to accelerated calcium transient decay observed experimentally.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Chemistry, Physical
Christian Seitz, Ilker Deveci, J. Andrew McCammon
Summary: This study investigates how protein glycosylation and lateral crowding effects modulate the stability and dynamics of influenza neuraminidase. The results show that glycans stabilize the protein structure, while a crowded membrane environment encourages large-scale conformational changes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)