Review
Biochemistry & Molecular Biology
Emery T. Usher, Scott A. Showalter
Summary: PDX1 is a central regulator of insulin transcription in pancreatic beta cells, and its function is regulated by cellular cues. However, the molecular mechanisms of PDX1 in glucose response remain elusive. This review summarizes existing studies on PDX1 and provides a comprehensive resource for future research on transcriptional control.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Entomology
Michael E. Scharf, Brittany F. Peterson
Summary: Termites and their symbiotic relationships with gut microbes have been studied extensively, with early research focusing on microscopy and organismal studies to understand the roles of symbionts in lignocellulose digestion. Advances in omic technologies have exponentially increased our knowledge of termite symbiosis, revealing the identities, functions, and interdependence of symbionts, as well as the complexities of host-symbiont complementarity. The merging of classical twentieth-century approaches with evolving omic tools is expected to provide even deeper insights into the interplay between hosts and symbionts.
ANNUAL REVIEW OF ENTOMOLOGY, VOL 66, 2021
(2021)
Article
Multidisciplinary Sciences
Kshitiz Parihar, Jonathan Nukpezah, Daniel Iwamoto, Paul A. Janmey, Ravi Radhakrishnan
Summary: Biomechanical signals from remodeled extracellular matrix (ECM) promote tumor progression. Cellular communication and interaction between cell-matrix and cell-cell may be influenced by mechanosensitive biogenesis of trafficking vesicles. Through machine learning, a fingerprint of cytoskeleton-related proteins has been identified to accurately characterize cell stiffness in different ECM conditions. The expression of these genes is correlated with patient prognosis across different tumor types. Cortical tension mirrors the changes in cell stiffness with a change in ECM stiffness. A mechanistic biophysical model shows that curvature generation is highly dependent on cortical tension. This study highlights the effect of ECM stiffness, mediated by cortical tension, in modulating vesicle biogenesis.
Article
Biochemistry & Molecular Biology
Anica Dadwal, Vishal Singh, Shilpa Sharma, Amaresh Kumar Sahoo, Tulasi Satyanarayana
Summary: This study analyzed the structure and thermostability of the cellulase CBHII from Mycoeliophthora thermophila using in-silico approaches. It found that the enzyme has a high affinity for cellotetraose and exhibits tolerance to elevated temperatures.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Physics, Multidisciplinary
Nesrine Aissa, Louis Douteau, Emmanuelle Abisset-Chavanne, Hugues Digonnet, Patrice Laure, Luisa Silva
Summary: In recent decades, significant advancements have been made in the field of scalable numerical tools and mesh immersion techniques to enhance numerical efficiency. A new octree-optimized microstructure generation and adaptive mesh domain reconstruction method has been proposed and demonstrated in a flow simulation example. By utilizing the parallel environment of the ICI-tech library, a large-scale case study was conducted.
Article
Biology
John V. V. Dzimianski, Julianna Han, Giuseppe A. A. Sautto, Sara M. M. O'Rourke, Joseph M. M. Cruz, Spencer R. R. Pierce, Jeffrey W. W. Ecker, Michael A. A. Carlock, Kaito A. A. Nagashima, Jarrod J. J. Mousa, Ted M. M. Ross, Andrew B. B. Ward, Rebecca M. M. DuBois
Summary: Structural studies of a computationally optimized broadly reactive antigen hemagglutinin in complex with a broadly neutralizing antibody reveal its immunogenic properties and provide insights into flu vaccine design.
COMMUNICATIONS BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Roy A. Quinlan, John I. Clark
Summary: In this review, the authors highlight the potential protective effects of post-translational modifications (PTMs) on lens proteins during normal development and propose a forward-looking hypothesis that aims to prevent age-related cataract (ARC) by protecting the biochemical and biophysical properties of lens proteins.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biology
Imtiaz Ali, Abbas Khan, Zhang Fa, Taimoor Khan, Dong-Qing Wei, Jianting Zheng
Summary: Acetyl-CoA carboxylase (ACC) plays a crucial role in polyketides biosynthesis and it is a promising drug target against obesity, cancer, microbial infections, and diabetes. However, the lack of knowledge about the relationship between ACC ligand-enzyme binding has hindered the development of ACC-specific therapeutics and unnatural polyketides. In this study, the crystal structure of AccB from Streptomyces antibioticus was determined to understand the substrate specificity and the molecular mechanism of acetyl-CoA recognition and processing. Key residues for substrate recognition were identified, and the atomic-level knowledge of substrate binding was provided, which will aid in the re-design of ACCs active site for efficient substrate specificity and diverse polyketide production.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Analytical
Jia-Dong Li, Guang-Pei Wu, Li-Hua Li, Lan-Teng Wang, Yi-Fan Liang, Ru-Yu Fang, Qiu-Ling Zhang, Ling-Ling Xie, Xing Shen, Yu-Dong Shen, Zhen-Lin Xu, Hong Wang, Bruce D. D. Hammock
Summary: This study elucidates the structural basis of the unique physicochemical properties and recognition mechanism of Nanobodies (Nbs) using an anti-quinalphos Nb as a model. The Nb-11A-ligand complexes exhibit a tunnel binding mode formed by CDR1, CDR2, and FR3. The affinity of small ligands to Nb-11A is primarily determined by their orientation and hydrophobicity. Furthermore, the rearrangement of the hydrogen bonding network and enlargement of the binding cavity contribute to limited stability of Nb-11A at high temperatures and in organic solvents. Key residues at the active cavity's bottom and entrance play vital roles in hapten recognition.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Ayushi Mishra, Amit Sharma, Suneel Kateriya
Summary: The study found that LOV proteins detect blue light by forming a covalent 'photoadduct' between the flavin chromophore and a conserved cysteine residue. However, proteins lacking this cysteine can still have functional response by forming a neutral flavin radical. Recent research has shown that tryptophan residue serves as the primary electron donor.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2023)
Review
Chemistry, Analytical
Puneet Mishra, Ramin Nikzad-Langerodi, Federico Marini, Jean Michel Roger, Alessandra Biancolillo, Douglas N. Rutledge, Santosh Lohumi
Summary: Calibration transfer (CT) involves chemometric techniques for transferring calibration models between spectrometers. Recent advancements have introduced new concepts for standard-free CT, showing potential for enhancing the sharing of calibration models between analytical devices.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Huayi Liu, Yi Zhou, Yingjie Song, Qianqian Zhang, Yeyi Kan, Xinyue Tang, Qingjie Xiao, Qianyin Xiang, Huanxiang Liu, Yunzi Luo, Rui Bao
Summary: CRISPR-Cas9 from Streptococcus pyogenes is a powerful biotechnological tool for DNA sequence modification. Understanding the dynamic mechanism of the REC lobe is crucial for designing and engineering better Cas9 enzymes. The structure analysis of the xCas9 P411T variant and molecular dynamics simulations revealed the central role of REC1 in the activation and target site binding process of Cas9.
Article
Biochemistry & Molecular Biology
Maria Georgina Herrera, Maria Julia Amundarain, Javier Santos
Summary: This study characterized and compared the nuclear localization signal of TDP-43, and results showed that this region has conformational plasticity, which is potentially enhanced by the nuclear localization signal.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Engineering, Environmental
Jiaxun Sun, Xinmiao Huang, Xiaoyong Song, Rui Tang, Menglu Zhao, Boya Cai, Huijuan Wang, Zilin Han, Yafeng Liu, Zhengqiu Fan
Summary: This study developed an improved health risk assessment model by combining two-dimensional Monte Carlo simulation and a Logistic Chaotic sequence based on published data from 2000 to 2021, in order to assess the potential health risks of trace metal(loid)s in soils to humans. The results showed that children and adult females were the high-risk populations for non-carcinogenic and carcinogenic risks, respectively. The study also identified priority control trace metals for different regions in China. Compared to traditional health risk assessment, the improved model increased assessment accuracy and provided recommended exposure parameters for high-risk populations.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Chemistry, Medicinal
Afrah Khairallah, Caroline J. Ross, Ozlem Tastan Bishop
Summary: Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) is a crucial enzyme involved in the biosynthesis of folate and tetrahydrobiopterin, essential for DNA replication, cell division, and neurotransmitter production. Understanding the intrinsic dynamics and allosteric modulation of GCH1 structure has potential implications for developing new antineuropathic treatments and antimalarial drugs. The study identified key sites regulating the GCH1 enzyme activity and proposed a starting point for drug development targeting neuropathic disorders and malaria.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Letter
Biochemistry & Molecular Biology
Vivek S. Bharadwaj, Brandon C. Knott, Jerry Stahlberg, Gregg T. Beckham, Michael F. Crowley
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemical Research Methods
Malcolm A. O'Neill, Ian Black, Breeanna Urbanowicz, Vivek Bharadwaj, Mike Crowley, Sabina Koj, Maria J. Pena
Article
Chemistry, Medicinal
Japheth E. Gado, Gregg T. Beckham, Christina M. Payne
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Multidisciplinary
Thomas Elder, Jose C. del Rio, John Ralph, Jorge Rencoret, Hoon Kim, Gregg T. Beckham, Michael F. Crowley
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2020)
Article
Multidisciplinary Sciences
Brandon C. Knott, Erika Erickson, Mark D. Allen, Japheth E. Gado, Rosie Graham, Fiona L. Kearns, Isabel Pardo, Ece Topuzlu, Jared J. Anderson, Harry P. Austin, Graham Dominick, Christopher W. Johnson, Nicholas A. Rorrer, Caralyn J. Szostkiewicz, Valerie Copie, Christina M. Payne, H. Lee Woodcock, Bryon S. Donohoe, Gregg T. Beckham, John E. McGeehan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Chemistry, Multidisciplinary
Laura Berstis, Thomas Elder, Richard Dixon, Michael Crowley, Gregg T. Beckham
Summary: The study suggests that increasing the concentration of flavonoids in lignin may lead to linkage properties conducive to more facile lignin depolymerization, thus improving the efficiency of utilizing lignocellulosic feedstocks in the bioeconomy.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Chemistry, Physical
Rodrigo L. Silveira, Brandon C. Knott, Caroline S. Pereira, Michael F. Crowley, Munir S. Skaf, Gregg T. Beckham
Summary: Serine hydrolases cleave peptide and ester bonds using a serine-histidine-aspartate/glutamate catalytic triad, with the critical role of the histidine residue undergoing conformational changes and proton transfer during the reaction. Active-site dynamics play a pivotal role in the catalytic mechanism of serine hydrolases, as shown in the case of AnFaeA.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Japheth E. Gado, Brent E. Harrison, Mats Sandgren, Jerry Stahlberg, Gregg T. Beckham, Christina M. Payne
Summary: GH7 family glycoside hydrolases are key enzymes in cellulose degradation, including cellobiohydrolases and endoglucanases. Machine-learning models show that the number of residues in the active-site loops strongly correlates with functional subtype across the GH7 family, with specific residues at certain sequence positions accurately predicting the subtype. Additionally, a random forest model trained on residues in the catalytic domain can predict the presence of a carbohydrate-binding module with high accuracy.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
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
Chemistry, Multidisciplinary
Young-Hoon Kim, Ruyi Song, Ji Hao, Yaxin Zhai, Liang Yan, Taylor Moot, Axel F. Palmstrom, Roman Brunecky, Wei You, Joseph J. Berry, Jeffrey L. Blackburn, Matthew C. Beard, Volker Blum, Joseph M. Luther
Summary: This study investigates how chiral ligands attached to perovskite nanocrystal surfaces distort the perovskite lattice and demonstrates the resulting chiral electro-optical properties. The major finding is a centro-asymmetric distortion of the surface lattice, which is likely the cause of the chiral-optical properties. Spin-polarized transport through chiral nanocrystals amplifies the discrimination between left and right-handed circularly polarized light.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Editorial Material
Chemistry, Physical
John M. Herbert, Martin Head-Gordon, Hrant P. Hratchian, Teresa Head-Gordon, Rommie E. Amaro, Alan Aspuru-Guzik, Roald Hoffmann, Carol A. Parish, Christina M. Payne, Troy Van Voorhis
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Topi Haataja, Japheth E. Gado, Anu Nutt, Nolan T. Anderson, Mikael Nilsson, Majid Haddad Momeni, Roland Isaksson, Priit Valjamae, Gunnar Johansson, Christina M. Payne, Jerry Stahlberg
Summary: In this study, the hydrolysis characteristics of two model enzymes in the CBH family 7 were examined using enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies. The results revealed that the strength of non-productive binding is a key determinant for the activity characteristics of these enzymes on different substrates.
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
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, 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)