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Multidisciplinary Sciences
Saminathan Ramakrishnan, Jason R. Stagno, Chelsie E. Conrad, Jienyu Ding, Ping Yu, Yuba R. Bhandari, Yun-Tzai Lee, Gary Pauly, Oleksandr Yefanov, Max O. Wiedorn, Juraj Knoska, Dominik Oberthuer, Thomas A. White, Anton Barty, Valerio Mariani, Chufeng Li, Wolfgang Brehm, William F. Heinz, Valentin Magidson, Stephen Lockett, Mark S. Hunter, Sebastien Boutet, Nadia A. Zatsepin, Xiaobing Zuo, Thomas D. Grant, Suraj Pandey, Marius Schmidt, John C. H. Spence, Henry N. Chapman, Yun-Xing Wang
Summary: Time-resolved crystallography is typically used to monitor small conformational changes within biomacromolecules in the same lattice. This study reveals the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, laying the foundation for investigating large conformational changes using time-resolved crystallography.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Zahra Musavizadeh, Alessandro Grottesi, Giulia Guarguaglini, Alessandro Paiardini
Summary: The study reveals the impact of phosphorylation on the stability of the A-loop and the effect of conformation disrupting inhibitors on the dynamics of Aurora-A. The presence of a phosphate moiety induces Aurora-A to sample two distinct energy minima, indicating a significant difference in conformational distributions compared to the unphosphorylated state.
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Biochemistry & Molecular Biology
Chiung-Fang Hsu, Kai-Chun Chang, Yi-Lan Chen, Po-Szu Hsieh, An- Lee, Jui-Yun Tu, Yu-Ting Chen, Jin-Der Wen
Summary: Programmed-1 ribosomal frameshifting in viruses and bacteria is stimulated by mRNA structures within the coding region. The RNA pseudoknot folds sequentially through upstream stem S1 and downstream stem S2, with S2 tending to be trapped in intermediates. Masking nucleotides can modulate mRNA refolding and facilitate the stable folding of native pseudoknots.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Erin R. Birdsall, Megan K. Petti, Vivek Saraswat, Joshua S. Ostrander, Michael S. Arnold, Martin T. Zanni
Summary: The study demonstrates that voltage-dependent structures of membrane-bound polypeptide alamethicin can be measured using a spectroelectrochemical cell with a rough gold film, revealing changes in structure under different voltage and pH conditions. The 2D IR spectra can resolve features between different helical structures, providing new structural information for voltage-gated membrane proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Justin Kurian, Veronica Bohl, Michael Behanan, Sadia Mohsin, Mohsin Khan
Summary: Metabolism plays a crucial role in regulating stem cell properties, with metabolites acting as secondary messengers in response to microenvironment changes. The study highlights the impact of acetyl-CoA on chromatin remodeling, particularly in cardiac cells. The differences in metabolism between neonatal cardiac stem cells and aged cardiac stem cells suggest a link between metabolism and chromatin remodeling with age.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ila A. Marathe, Stella M. Lai, Walter J. Zahurancik, Michael G. Poirier, Vicki H. Wysocki, Venkat Gopalan
Summary: The ribonucleoprotein form of archaeal RNase P consists of one catalytic RNA and five protein cofactors, which work together to recognize and cleave tRNA in a Mg2+-dependent manner. The addition of RPPs decreases the Mg2+ requirement and improves cleavage efficiency. Mg2+ and RPP proteins play essential roles in enhancing activity by inducing structural changes in RNA.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Jixing Zhang, Tianyi Ding, He Zhang
Summary: cheRNAs are a special class of long noncoding RNAs that are enriched around chromatin and regulate the transcription of neighboring or distal genes by affecting chromatin structure and gene expression. Abnormal transcription of cheRNAs plays a critical role in the occurrence of diseases, particularly tumors. The specific role of cheRNAs in tumorigenesis, especially in cancer stem cell proliferation and stemness maintenance, is still not fully understood.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Environmental Sciences
Wanying Sun, Lei Wang
Summary: This study diagnosed the temporal evolution of winter Northern Hemisphere stationary waves during 1961-2020 using ERA5 data, showing an overall strengthening in amplitude and an eastward shift in phase. The changes in stationary waves are primarily driven by the zonal mean basic state and the zonally asymmetric diabatic heating forcing.
ENVIRONMENTAL RESEARCH LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Chang Liu, Zhizhen Li, Zonghan Liu, Shiye Yang, Qing Wang, Zongtao Chai
Summary: This study revealed the conformational dynamics of the phosphate-binding loop (P-loop) in different states of STK17B through molecular dynamics simulation. The interactions between the P-loop and inhibitors were found to contribute to inhibitor selectivity profile. These findings advance our understanding of kinase inhibitor selectivity and have implications for the design of selective inhibitors for other protein kinases.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
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Biology
Chiyu Zhang, Donald R. Forsdyke
Summary: Both HIV-1 and SARS-CoV-2 have highly conserved regions that can be targeted by specific antiviral drugs, which may be their potential Achilles' heels. The structural invariance of these regions may be sustained by natural selection.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Xiaohong Wang, Jianping Da, Yuanjian Liu
Summary: An electrochemical biosensor for staphylococcal enterotoxin B (SEB) detection has been designed based on the electrochemical interrogation of conformational changes, showing high sensitivity and accuracy.
Article
Chemistry, Physical
Yi Dong, Lei Fu, Junjie Song, Shan Zhang, Xiangyuan Li, Weihai Fang, Qiang Cui, Lianghui Gao
Summary: The study revealed that calcium ions have the highest binding affinity to a zwitterionic phospholipid bilayer, while magnesium and zinc ions' binding processes are exothermic and less preferred. Calcium ions release coordinated water upon binding, with less influence; while magnesium and zinc ions remain fully hydrated when interacting with lipids, making binding less favorable.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Review
Biochemistry & Molecular Biology
Ausra Domanska, Sergey Guryanov, Sarah J. Butcher
Summary: Parechoviruses are non-enveloped icosahedral viruses with a single-stranded RNA genome, infecting humans and causing a range of illnesses. There are currently no approved antivirals for treating parechovirus infections.
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Chemistry, Analytical
Helisa H. Wippel, Juan D. Chavez, Andrew D. Keller, James E. Bruce
Summary: The XL-MS technique provides insight into protein conformations and interactions within their cellular environment, while the iqPIR strategy allows for comparative interactome studies using isotope encoded chemical cross-linkers. Multiplexed iqPIR enables quantitative interactome analysis of up to six biological samples in a single LC-MS acquisition, revealing specific protein conformational and interaction changes in response to different inhibitors.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Cristina Romero-Lopez, Alfredo Berzal-Herranz, Jose Luis Martinez-Guitarte, Mercedes de la Fuente
Summary: The telomeric transcriptome of Chironomus riparius is involved in thermal stress response, with the CriTER-A variant highly overexpressed during heat shock compared to the less affected CriTER-B variant. The study suggests that CriTER-A folds into two different conformers under temperature conditions, while CriTER-B variant exhibits a single dominant conformer. This temperature-dependent conformational equilibrium of CriTER-A may indicate a potential functional role of the telomeric transcriptome in response to thermal stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Arthur J. Campbell, Carlos de los Santos, Arthur Grollman, Dmitry O. Zharkov, Carlos Simmerling
NUCLEIC ACIDS RESEARCH
(2016)
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Biochemistry & Molecular Biology
Hamed S. Hayatshahi, Christina Bergonzo, Thomas E. Cheatham
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2018)
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Chemistry, Multidisciplinary
Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman, Dmitry O. Zharkov, Carlos Simmerling
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Biochemistry & Molecular Biology
Christina Bergonzo, Alexander Grishaev
JOURNAL OF BIOMOLECULAR NMR
(2019)
Article
Biochemistry & Molecular Biology
Christina Bergonzo, Alexander Grishaev
JOURNAL OF STRUCTURAL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Erik M. Leith, William B. O'Dell, Na Ke, Colleen McClung, Mehmet Berkmen, Christina Bergonzo, Robert G. Brinson, Zvi Kelman
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Christina Bergonzo, Kunal Dharmadhikari, Emily Samuels, Makenzie Christensen, Jennifer Tullman
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Christina Bergonzo, Andrea L. Szakal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Instruments & Instrumentation
Christina Bergonzo, D. Travis Gallagher
JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Daniel R. Roe, Christina Bergonzo
Summary: This tool can automatically identify various properties of carbohydrates and generate the necessary commands and files, simplifying the complexity of setting up molecular dynamics simulations from experimentally determined structures.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Christina Bergonzo, Alexander Grishaev, Sandro Bottaro
Summary: We describe the conformational ensemble of a single-stranded oligonucleotide using MD simulations and the FARFAR2 algorithm. The presence of A-form-like structures and other extended conformations is necessary to explain experimental data. However, simulations result in more compact structures than observed in experiments. Integration of simulations with NMR data improves the description of the conformational ensemble, but discrepancies with experimental SAXS data persist.
Article
Biochemical Research Methods
Christina Bergonzo, Baikuntha Aryal, V. Ashutosh Rao
Summary: The toxicity caused by off-pathway reactions can limit the dosing and efficacy of chemotherapeutic drugs. Metal-catalyzed oxidative damage of cardiac myosin binding protein C (cMyBP-C) in cardiac tissue is one potential mechanism for such toxicity. This study investigates the ion environment surrounding specific subunits of cMyBP-C responsible for actin binding and reveals the potential interruption of actin-cMyBP-C binding due to protein carbonylation in these subunits.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
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Chemistry, Physical
Danielle Schultz, Robert G. Brinson, Nese Sari, Jeffrey A. Fagan, Christina Bergonzo, Nancy J. Lin, Joy P. Dunkers
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Biophysics
Christina Bergonzo, Thomas E. Cheatham
BIOPHYSICAL JOURNAL
(2017)