Article
Multidisciplinary Sciences
Navid Paknejad, Vinay Sapuru, Richard K. Hite
Summary: IP3R receptors are endoplasmic reticulum Ca2+ channels that exhibit biphasic dependence on cytosolic Ca2+, leading to Ca2+ oscillations that regulate various cellular processes. This study reveals that Ca2+ binding does not induce explicit conformational changes, but biases a complex conformational landscape of the receptor. High-affinity Ca2+ binding allows the receptor to escape a low-energy resting state and activate through a series of preactivated states. At high Ca2+ concentrations, the receptor enters an inhibited state stabilized by a low-affinity Ca2+ binding site.
NATURE COMMUNICATIONS
(2023)
Article
Evolutionary Biology
Michael Lynch, Zhiqiang Ye, Lina Urban, Takahiro Maruki, Wen Wei
Summary: By analyzing the whole genome of a microcrustacean, researchers have discovered certain characteristics of the recombination landscape in gene evolution, such as the uniformity of recombination rates, consistent patterns of linkage disequilibrium, and the involvement of recombination mechanisms unrelated to crossing-over. These findings challenge the traditional LD equilibrium model.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Physics, Multidisciplinary
Rafael Tapia-Rojo, Marc Mora, Stephanie Board, Jane Walker, Rajaa Boujemaa-Paterski, Ohad Medalia, Sergi Garcia-Manyes
Summary: By using single-molecule magnetic tweezers, researchers have observed previously inaccessible rare conformations of the talin protein and investigated its folding dynamics over extended periods of time. This study sheds light on the complex landscapes of protein folding and highlights the importance of observation timescale in understanding equilibrium dynamics.
Article
Multidisciplinary Sciences
Rahil Taujale, Zhongliang Zhou, Wayland Yeung, Kelley W. Moremen, Sheng Li, Natarajan Kannan
Summary: The study utilizes interpretable deep learning to predict the folds of glycosyltransferases (GTs) without the need for sequence alignment, enabling the prediction of GTs with new folds.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yongsheng Li, Brandon Burgman, Ishaani S. Khatri, Sairahul R. Pentaparthi, Zhe Su, Daniel J. McGrail, Yang Li, Erxi Wu, S. Gail Eckhardt, Nidhi Sahni, S. Stephen Yi
Summary: Understanding the functional impact of cancer somatic mutations is important for precision oncology. The e-MutPath network-based computational method can identify candidate mutations that perturb functional pathways, distinguish disease risk factors from neutral elements, and stratify disease subtypes with clinical relevance. This tool represents a powerful way to systematically assign functions to genetic mutations in the context of their pathway perturbation effect.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Chisae Nagiri, Kazuhiro Kobayashi, Atsuhiro Tomita, Masahiko Kato, Kan Kobayashi, Keitaro Yamashita, Tomohiro Nishizawa, Asuka Inoue, Wataru Shihoya, Osamu Nureki
Summary: The study presents the detailed structure of β(3)AR and reveals a receptor activation mechanism upon binding of an agonist, providing a molecular basis for the design of more-selective agents with fewer adverse effects.
Article
Chemistry, Medicinal
David Shorthouse, Michael W. J. Hall, Benjamin A. Hall
Summary: Single amino acid substitutions within proteins can lead to clinical conditions in humans, with tools from chemical engineering being developed to predict the impact of point mutations and guide protein design. By adapting these tools for predicting damaging mutations in proteins like fumarate hydratase (FH), and using techniques like molecular dynamics simulations, researchers can accurately predict the clinical effects of specific mutations and hotspots in FH. This can provide insights into the functional implications of mutations on the enzyme and categorize potential mutations into functional groups with clinical significance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Rebecca Conners, Rayen Ignacia Leon-Quezada, Mathew McLaren, Nicholas J. Bennett, Bertram Daum, Jasna Rakonjac, Vicki A. M. Gold
Summary: Phages, viruses that infect bacteria, are prevalent in every ecosystem on Earth and have various applications in molecular biology and biotechnology. The structure and mechanisms of infection and assembly of filamentous phages, particularly the Ff phages, have been largely unknown. In this study, the researchers used cryo-electron microscopy and a highly efficient system to produce short Ff-derived nanorods, successfully determining the structure of a filamentous virus including the tips. By combining the structure with mutagenesis, they identified important phage domains involved in bacterial attack and release of new viral progeny, leading to the proposal of new models for the phage lifecycle.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Eman Alnabati, Juan Esquivel-Rodriguez, Genki Terashi, Daisuke Kihara
Summary: In this study, a method using Markov random fields to fit protein atomic structures into low-resolution cryo-EM maps was designed. The accuracy of this method, called MarkovFit, outperformed existing methods on multiple datasets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Austin S. Draycott, Cassandra Schaening-Burgos, Maria F. Rojas-Duran, Loren Wilson, Leonard Scharfen, Karla M. Neugebauer, Sigrid Nachtergaele, Wendy Gilbert
Summary: The study introduces a new sequencing technique called D-seq to map dihydrouridine (D) with single-nucleotide resolution in the transcriptome. Novel classes of D-containing RNA, including mRNA and snoRNA, are discovered in yeast. The D sites are concentrated in conserved stem-loop regions and are involved in splicing of pre-mRNA and translation of mRNA.
Article
Biology
Dawn M. Wenzel, Douglas R. Mackay, Jack J. Skalicky, Elliott L. Paine, Matthew S. Miller, Katharine S. Ullman, Wesley Sundquist, Aurelien Roux
Summary: In this study, the interactions between human MIT domains and ESCRT-III tails were comprehensively mapped and quantified. Several new interactions were discovered, and the structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail was reported. The study also revealed the localization and functions of three MIT enzymes in cytokinetic abscission.
Article
Physics, Multidisciplinary
Yan Fyodorov, Rashel Tublin
Summary: In this study, we analyze the statistical features of the 'optimization landscape' in a basic constrained optimization problem and derive the exact expressions for key metrics of the problem. These findings provide important insights for solving the problem numerically.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Biodiversity Conservation
H. Patrick Roberts, Michael T. Jones, Lisabeth L. Willey, Thomas S. B. Akre, Paul R. Sievert, Phillip DeMaynadier, Katharine D. Gipe, Glenn Johnson, John Kleopfer, Michael Marchand, Joshua Megyesy, Steven Parren, Edward Thompson, Chris Urban, Derek Yorks, Brian Zarate, Lori Erb, Angelena M. Ross, Jeffrey Dragon, Lori Johnson, Ellery Lassiter, Elliot Lassiter
Summary: Freshwater turtles and tortoises are facing a worldwide decline, with collaborative monitoring efforts revealing that mature forest cover positively impacts population demographics, while agriculture and road traffic have negative effects. Effective conservation strategies for demographically robust turtle populations require consideration of multiple spatial scales.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Biochemistry & Molecular Biology
Taivan Batjargal, Francesca Zappa, Ryan J. Grant, Robert A. Piscopio, Alex Chialastri, Siddharth S. Dey, Diego Acosta-Alvear, Maxwell Z. Wilson
Summary: The integrated stress response (ISR) is a signaling network that detects aberrations and computes cellular responses. By engineering a photo-switchable control over the ISR sensor kinase PKR (opto-PKR), we traced information flow through the transcriptome and identified two dynamic modes of transcriptional response. An ordinary differential equation (ODE) model of the ISR demonstrated the dependence of future stress responses on past stress. Our results showed that cells encode information in stress levels, durations, and timing between encounters.
Article
Forestry
George Kefalas, Roxanne Suzette Lorilla, Panteleimon Xofis, Konstantinos Poirazidis, Nicolas-George Homer Eliades
Summary: The Mediterranean area is highly impacted by human activity, leading to altered biodiversity and complex socioecological systems. Understanding the factors that influence the supply of ecosystem services is crucial for effective forest management policies that ensure both ecological integrity and human welfare.
Article
Chemistry, Multidisciplinary
Inha Cho, Christopher K. Prier, Zhi-Jun Jia, Ruijie K. Zhang, Tamas Gorbe, Frances H. Arnold
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Multidisciplinary Sciences
Ruijie K. Zhang, Kai Chen, Xiongyi Huang, Lena Wohlschlager, Hans Renata, Frances H. Arnold
Article
Chemistry, Organic
Kai Chen, Xiongyi Huang, Shuo-Qing Zhang, Andrew Z. Zhou, S. B. Jennifer Kan, Xin Hong, Frances H. Arnold
Article
Chemistry, Multidisciplinary
Xiongyi Huang, Marc Garcia-Borras, Kun Miao, S. B. Jennifer Kan, Arjun Zutshi, K. N. Houk, Frances H. Arnold
ACS CENTRAL SCIENCE
(2019)
Review
Biochemistry & Molecular Biology
Ruijie K. Zhang, Xiongyi Huang, Frances H. Arnold
CURRENT OPINION IN CHEMICAL BIOLOGY
(2019)
Article
Chemistry, Multidisciplinary
Oliver F. Brandenberg, Kai Chen, Frances H. Arnold
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Multidisciplinary Sciences
Zachary Wu, S. B. Jennifer Kan, Russell D. Lewis, Bruce J. Wittmann, Frances H. Arnold
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Chemistry, Multidisciplinary
Juner Zhang, Xiongyi Huang, Ruijie K. Zhang, Frances H. Arnold
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Biochemistry & Molecular Biology
Ella J. Watkins, Patrick J. Almhjell, Frances H. Arnold
Article
Chemistry, Physical
David K. Romney, Nicholas S. Sarai, Frances H. Arnold
Article
Chemistry, Physical
Oliver F. Brandenberg, David C. Miller, Ulrich Markel, Anissa Ouald Chaib, Frances H. Arnold
Article
Chemistry, Multidisciplinary
Frances H. Arnold
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Biochemical Research Methods
Claire N. Bedbrook, Kevin K. Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Article
Chemistry, Multidisciplinary
Nathaniel W. Goldberg, Anders M. Knight, Ruijie K. Zhang, Frances H. Arnold
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Review
Chemistry, Physical
Kai Chen, Frances H. Arnold