Article
Chemistry, Multidisciplinary
Tina Jeoh, Jennifer Danger Nill, Wujun Zhao, Sankar Raju Narayanasamy, Liang Chen, Hoi-Ying N. Holman
Summary: In this study, the enzymatic hydrolysis of cellulose was investigated using real-time infrared spectromicroscopy. The spatial heterogeneity of cellulose was found to impact the hydrolysis kinetics. Hydration affected cellulose ordering, and Cel7A preferentially removed less extensively hydrogen bonded cellulose.
Article
Mechanics
P. M. Ndiaye, F. W. Tavares, E. K. Lenzi, L. R. Evangelista, H. Ribeiro, D. Marin, L. M. S. Guilherme, R. S. Zola
Summary: The study focuses on the modeling of diffusion and trapping of particles inspired by biology and natural behavior, particularly in systems connected by surfaces to bulk, such as living cells and biomaterials. The research finds a variety of behaviors through analytical calculations and computer simulations, showing a good agreement between the two methods.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Review
Chemistry, Multidisciplinary
Abraham Muniz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade
Summary: Brownian dynamics (BD) is a computational method used to simulate molecular diffusion processes, and recent developments have improved its accuracy and expanded its applications. In biological research, BD is used to study the diffusive behavior of molecules under various conditions and to compute rate constants for molecular association and examine transport properties. The development of software packages for BD simulations has provided new features and expanded the range of questions that can be addressed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
Thorsten Prustel, Martin Meier-Schellersheim
Summary: This study focused on computational models of reaction-diffusion systems commonly found in cellular signaling pathways, and introduced an approach that allows for the reconstruction of entire molecular trajectories after a simulated time step, avoiding the need for inefficient draws from non-standard distributions. This method enables highly accurate stochastic simulations for system sizes that would be prohibitively costly to simulate with conventional Green's function based methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Agricultural Engineering
Jie Wu, Yintian Dong, Huaiyu Zhang, Jingyun Liu, Scott Renneckar, Jack Saddler
Summary: Enzyme-mediated cellulose hydrolysis initially proceeds rapidly but gradually slows down, leading to incomplete hydrolysis even after prolonged incubation. The main mechanism for this appears to be reduced accessibility of cellulose to the enzymes. Washing residual cellulose increases accessibility by removing tightly bound non-productive enzymes, while atomic force microscopy analysis shows increased roughness of the cellulose surface during hydrolysis, potentially leading to tighter binding of less active cellulases.
BIORESOURCE TECHNOLOGY
(2023)
Article
Agricultural Engineering
Manish Paul, Sonali Mohapatra, Pradeep Kumar Das Mohapatra, Hrudayanath Thatoi
Summary: Efficient degradation of lignocellulosic biomass requires adjustments to the surface charge of cellulases, maintenance of their secondary structure, and enhancement of catalytic activity, with the use of computational design for improved efficiency. Genetic engineering for tailored genes can increase cellulase production efficiency, and improving recovery rates can lead to larger scale enzyme production.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sutapa Dutta, Mariacristina Gagliardi, Luca Bellucci, Matteo Agostini, Stefano Corni, Marco Cecchini, Giorgia Brancolini
Summary: This study presents a rationally designed gold-functionalized surface capable of capturing a target protein using the biotin-streptavidin pair. Through multiscale simulations and experimental comparisons, they found a specific mechanism and provided guidelines for designing biosensors with enhanced sensitivity.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Materials Science, Paper & Wood
Sathish Kumar Mudedla, Maisa Vuorte, Elias Veijola, Kaisa Marjamaa, Anu Koivula, Markus B. Linder, Suvi Arola, Maria Sammalkorpi
Summary: Enzymatic cleavage of glycocidic bonds is an important method to refine lignocellulosic biomass. This study explored the effects of oxidation defects on the structure and water interactions of cellulose {100} surface, showing that even single oxidations reduce connections within cellulose crystal and enhance water interactions. The findings also revealed different levels of soluble glucose fragments released during LPMO enzyme treatment on different cellulose species, indicating the significance of understanding enzymatic oxidation effects on cellulose nanocrystals and cleavage of soluble products.
Article
Physics, Multidisciplinary
Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake, Ralf Metzler
Summary: The study demonstrates that protein conformational fluctuations directly affect the diffusion properties, showing synchronous fluctuations with diffusivity. The radius of gyration of proteins exhibits 1/f fluctuations. The validity of the Stokes-Einstein-type relation appears to be a general property based on analysis of different protein types.
PHYSICAL REVIEW LETTERS
(2021)
Article
Agricultural Engineering
Xiaoxue Zhao, Caoxing Huang, Wenqian Lin, Bin Bian, Chenhuan Lai, Zhe Ling, Qiang Yong
Summary: This study investigated the adsorption mechanism and structure-activity relationship between lignin and different cellulase domains using fluorescence spectroscopy and SDS-PAGE. It was found that endo-cellulase 6B had a higher affinity to lignin fractions, which was positively correlated to molecular weight. The adsorption between lignin fractions and endo-cellulase 6B was mainly driven by van der Waals and electrostatic forces, while hydrophobic force drove the adsorption of lignin fractions to CBM4A. The results demonstrated the critical role of lignin's structure in its adsorption with various cellulase domains.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Applied
Tian Liu, Yu Zhang, Xiaomin Lu, Peipei Wang, Xinyu Zhang, Jing Tian, Qingcheng Wang, Junlong Song, Yongcan Jin, Huining Xiao
Summary: CBM4 binds preferentially to both CNF and CNC, with different driving forces: hydrogen bonds for CNF resulting in favorable enthalpy but compensated by unfavorable entropy change, while favorable entropy for CNC but compensated by unfavorable enthalpic change due to water rearrangement.
CARBOHYDRATE POLYMERS
(2021)
Article
Chemistry, Physical
Tetsuro Nagai, Akira Yoshimori, Susumu Okazaki
Summary: This study investigates a series of new Monte Carlo transition probabilities that can simulate molecular trajectories satisfying the diffusion equation. The results show good agreement with the numerical solution. The method is useful for studying long-distance transport of molecules in heterogeneous systems and many-particle dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Cihan Ayaz, Laura Scalfi, Benjamin A. Dalton, Roland R. Netz
Summary: We present a hybrid projection scheme that combines linear Mori projection and conditional Zwanzig projection techniques to derive a generalized Langevin equation (GLE) for a general interacting many-body system. The resulting GLE includes the potential of mean force (PMF) that describes the equilibrium distribution of the system, a random force term that depends on the initial state of the system, and a memory friction contribution. Our hybrid scheme combines desirable properties of Zwanzig and Mori projection schemes. The nonlinear memory friction contribution is related to correlations between the reaction-coordinate velocity and the random force.
Article
Biochemistry & Molecular Biology
Junzhao Yang, Xinrui Zhang, Qingyang Sun, Ruilin Li, Xiaoyu Wang, Guozhu Zhao, Xiangwei He, Fei Zheng
Summary: This study identified two structural elements related to the catalysis and thermostability of TtCel7 through structure-directed enzyme modulation. The B3 loop of TtCel7 possibly stretches the catalytic pocket, increasing the openness of the catalytic tunnel and enhancing flexibility for efficient catalysis. Additionally, the disulfide bond within the B3 loop serves to enhance structural stability and maintain a heightened level of activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Engineering, Biomedical
Mariana Barbosa, Helvio Simoes, Sandra N. Pinto, Ana S. Macedo, Pedro Fonte, D. Miguel F. Prazeres
Summary: The study proposes a new strategy to modify cellulose-based materials with an antimicrobial peptide MP196 through a biomolecular recognition approach. The modified materials displayed significantly higher antibacterial activity against E. coli, P. aeruginosa, and S. aureus compared to materials prepared by physical adsorption of MP196. The biomolecular strategy provides a versatile concept for the functionalization of cellulose materials for various applications including drug delivery systems and tissue engineering.
ACTA BIOMATERIALIA
(2022)
Article
Biochemistry & Molecular Biology
Christopher M. Topham, Jeremy C. Smith
Summary: The study investigates the binding interactions between the E-base and thymine and uracil bases, finding significant strain energy in systems containing a beta-alanine linker, while the E-base swings away from the target bases into the solvent in systems containing a 3-trans olefin linker. Additionally, calculations on a novel 2-cis olefin linker design suggest potential simultaneous hydrogen bonding with the thymine 4-oxo group, circumvention of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Yulin Ren, Sijin Wu, Joanna E. Burdette, Xiaolin Cheng, A. Douglas Kinghorn
Summary: Digoxin, a cardiac glycoside, has been found to exhibit antitumor potential and its cytotoxicity is influenced by specific structural features and interactions with Na+/K+-ATPase. Docking studies also suggest that the docking scores of digoxin and its derivatives correlate with their cytotoxicity, indicating their potential use in predicting the cytotoxicity of other cardiac glycosides. Additionally, digoxin was found to directly target FIH-1, Na+/K+-ATPase, and NF-kappa B for its antitumor effects.
Article
Biochemistry & Molecular Biology
Vivek S. Bharadwaj, Luke P. Westawker, Michael F. Crowley
Summary: This study developed a computational approach to predict the NMR signals of Apiose-borate complexes and enhance the understanding of the structure of RG-II. The results demonstrate that considering implicit solvation during geometry optimization greatly improves the accuracy of NMR chemical shift predictions.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Engineering, Biomedical
Abhjeet S. Bhullar, Long Zhang, Nicolas Burns, Xiaolin Cheng, Peixuan Guo
Summary: Researchers have discovered and constructed a durable nanoscale bio-aperture that can regulate current at the pico-ampere scale. The aperture is made of 12 identical protein subunits and has a shutter and one-way traffic property. This discovery has important implications for nanodevices and disease diagnosis.
Article
Biochemistry & Molecular Biology
Josh V. Vermaas, Michael F. Crowley, Gregg T. Beckham
Summary: This study investigates the permeability of bacterial outer membrane to lignin-related compounds through simulations and finds that they have low permeation due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer. However, this effect is relatively modest at industrially relevant concentrations.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Zoe Li, Kevin C. Chan, Jonathan D. Nickels, Xiaolin Cheng
Summary: Biomolecular binding relies on specific attractive interactions between partner molecules. This study examines the electrostatic contributions to nicotine binding by simulating the binding free energy of nicotine and acetylcholine binding protein (AChBP). The simulations reveal that nicotine binds AChBP predominantly in its charged form, and the binding is driven by electrostatic interactions, cation-pi interactions, and hydrogen bonding. Van der Waals interactions also play a role in the binding process.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Viswanathan Gurumoorthy, Utsab R. Shrestha, Qiu Zhang, Sai Venkatesh Pingali, Eric T. Boder, Volker S. Urban, Jeremy C. Smith, Loukas Petridis, Hugh O'Neill
Summary: c-Src kinase is a non-receptor tyrosine kinase that phosphorylates signaling proteins in cancers. This study focuses on the N-terminal disordered region (SH4UD) and its interactions with other domains of c-Src kinase. The results show that the presence of SH4UD leads to structural changes in the regulatory domains (SH3-SH2), indicating the importance of the disordered region for allosteric interactions. This study provides insights that may aid in the development of therapeutic interventions targeting the regulatory domains of c-Src kinase.
Article
Chemistry, Multidisciplinary
Luoxi Tan, Haden L. Scott, Micholas Dean Smith, Sai Venkatesh Pingali, Hugh M. O'Neill, Jennifer L. Morrell-Falvey, John Katsaras, Jeremy C. Smith, Brian H. Davison, James G. Elkins, Jonathan D. Nickels
Summary: Biofuels are crucial for sustainable energy and optimizing their production is a societal and economic imperative. Reducing the toxicity of co-solvents can improve the efficiency of biofuel production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Taku Uchiyama, Takayuki Uchihashi, Takuya Ishida, Akihiko Nakamura, Josh V. Vermaas, Michael F. Crowley, Masahiro Samejima, Gregg T. Beckham, Kiyohiko Igarashi
Summary: Efficient depolymerization of crystalline cellulose requires the cooperative action of multiple cellulolytic enzymes. This study demonstrates that the synergistic activity between cellobiohy-drolases and a lytic polysaccharide monooxygenase can enhance the activity and performance of the enzymes by producing chain breaks and amorphizing the crystalline surface of cellulose.
Article
Chemistry, Medicinal
Zoe Li, Kevin C. Chan, Jonathan D. Nickels, Xiaolin Cheng
Summary: Pentameric ligand-gated ion channels, including 5-HT3 receptors, are important for fast neurotransmissions and clinical treatment of chemotherapy-induced nausea and vomiting. This study presents a refined equilibration protocol to stabilize open state structures of the 5-HT3 receptor, allowing water and ion permeation through the channel. The findings highlight the conformational coupling between transmembrane helices as crucial for achieving stable open-like structures.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Mood Mohan, Micholas Dean Smith, Omar Demerdash, Michelle K. Kidder, Jeremy C. Smith
Summary: Understanding the physical properties of ionic liquids is crucial for various industrial and research applications, but experimental screening can be challenging and expensive. Previous research has shown that combining quantum-mechanics-based property prediction tools with machine learning approaches can help screen and design ionic liquids with desired properties. However, the most appropriate machine learning approach is still unclear.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Plant Sciences
Yulin Ren, Elizabeth N. Kaweesa, Lei Tian, Sijin Wu, Kongmany Sydara, Mouachanh Xayvue, Curtis E. Moore, Djaja D. Soejarto, Xiaolin Cheng, Jianhua Yu, Joanna E. Burdette, A. Douglas Kinghorn
Summary: A cardiac glycoside epoxide, (-)-cryptanoside A (1), was isolated from Cryptolepis dubia and showed potent cytotoxicity against various human cancer cell lines. It also inhibited Na+/K+-ATPase activity and increased the expression of Akt and the p65 subunit of NF-κB. Molecular docking analysis suggested that (-)-cryptanoside A (1) directly targets Na(+)/K+-ATPase to exhibit its cytotoxic effects on cancer cells.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Chemistry, Multidisciplinary
Mood Mohan, Micholas Dean Smith, Omar N. Demerdash, Blake A. Simmons, Seema Singh, Michelle K. Kidder, Jeremy C. Smith
Summary: Ionic liquids (ILs) have unique solvent properties, but it is unrealistic to experimentally determine their physicochemical properties. To address this issue, we developed machine learning models to predict the surface tension and speed of sound of ILs, which showed excellent agreement with experimental observations. This study paves the way for the development of machine learning models for predicting IL properties.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Medicinal
Rupesh Agarwal, T. Rajitha Rajeshwar, Jeremy C. Smith
Summary: Structure-based virtual high-throughput screening is commonly used in early-stage drug discovery. This study evaluated the performance of three docking protocols on 173 RNA-small molecule crystal structures. The results showed that Vina and rDock are both applicable for projects without known ligand-protein structures, but their performance is relatively poor compared to protein-target docking methods.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Nicholas A. Rorrer, Sandra F. Notonier, Brandon C. Knott, Brenna A. Black, Avantika Singh, Scott R. Nicholson, Christopher P. Kinchin, Graham P. Schmidt, Alberta C. Carpenter, Kelsey J. Ramirez, Christopher W. Johnson, Davinia Salvachua, Michael F. Crowley, Gregg T. Beckham
Summary: This study highlights the potential of beta-ketoadipic acid (beta KA) as a performance-advantaged replacement for adipic acid in nylon-6,6 analog. It demonstrates that beta KA can improve the thermal properties and reduce water permeability of nylon-6,6. The study also shows the feasibility and economic viability of producing beta KA from glucose derived from biomass. This is of great importance for the development of bio-based polymers.
CELL REPORTS PHYSICAL SCIENCE
(2022)