Article
Multidisciplinary Sciences
Han Pan, Ruifang Guan, Ruixue Zhao, Guangshuo Ou, Zhucheng Chen
Summary: The central spindle in animal cells regulates the formation of the division plane during cytokinesis. The molecular backbone of centralspindlin has the propensity to undergo liquid-liquid phase separation, and the synergy between ZEN-4 and CYK-4 subunits is critical for its function in microtubule bundling and central spindle assembly. Charge-driven macromolecular condensation mediates the assembly of the central spindle by centralspindlin.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Sean P. Fagan, Purba Mukherjee, William J. Jaremko, Rachel Nelson-Rigg, Ryan C. Wilson, Tyler L. Dangerfield, Kenneth A. Johnson, Indrajit Lahiri, Janice D. Pata
Summary: Bacterial replication is primarily catalyzed by DNA polymerase III's alpha subunit, with the replicative polymerase PolC from Staphylococcus aureus able to recognize the next correct nucleotide in advance. By modulating the rate of pyrophosphate byproduct release, PolC can adjust DNA synthesis speed in response to diverse cellular environments, ensuring high fidelity replication.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Chemistry, Physical
Lalima K. K. Madan, Colin L. L. Welsh, Alexandr P. P. Kornev, Susan S. S. Taylor
Summary: Allosteric regulation of proteins is an engaging research topic that has evolved from focusing on structural changes to considering internal protein dynamics. The violin model, based on redistribution of protein thermal fluctuations, utilizes graph theory and community network analysis to cluster correlated protein motions. This Review provides the theory and workflow of the methodology and illustrates its application to protein kinase A.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Andreas Heerwig, Alfred Kick, Paul Sommerfeld, Sophia Eimermacher, Frederick Hartung, Markus Laube, Dietmar Fischer, Hans-Juergen Pietzsch, Jens Pietzsch, Reik Loeser, Michael Mertig, Markus Pietsch, Robert Wodtke
Summary: In addition to their traditional functions, proteins also undergo conformational remodeling which is closely related to their specific functions. Transglutaminase 2 (TGase 2), a protein involved in various pathophysiological processes, undergoes comprehensive conformational changes, motivating the development of theranostic agents. The use of switchSENSE((R)) principle and computational methods allows the detection and quantification of conformational changes in TGase 2 caused by specific inhibitors, providing valuable information for drug development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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)
Article
Biochemistry & Molecular Biology
Jixue Sun, Zibin Li, Na Yang
Summary: SMYD3 is a methyltransferase that catalyzes methylation of MAP3K2, which is implicated in Ras-driven tumorigenesis. Studies suggest that conformational changes may regulate its catalytic activity, and this mechanistic study provides insights into the relationship between conformational change and methyltransferase activity of SMYD3, laying a foundation for rational drug design of SMYD3 inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Ji Ma, Shudong Ma, Ying Zhang, Yi Shen, Lei Huang, Tianhao Lu, Lu Wang, Yunhan Wen, Zhenhua Ding
Summary: Depletion of kinectin1 (KTN1) inhibits tumorigenesis of cutaneous squamous cell carcinoma (cSCC) by reducing epidermal growth factor receptor (EGFR) protein levels. The underlying mechanism involves KTN1 knockdown promoting EGFR degradation in cSCC cells through the ubiquitin-proteasome system. KTN1 depletion also leads to tumor suppressor functions mediated by CCDC40, PSMA1, and ADRM1, providing novel insights into EGFR degradation in cSCC.
CELL DEATH & DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Manuela Pose, Kearsley M. Dillon, Ana Denicola, Beatriz Alvarez, John B. Matson, Matias N. Moeller, Ernesto Cuevasanta
Summary: The study presents a new quantification method based on pyrene excimers formation for detecting hydrogen sulfide (H2S) in biochemical systems. The method utilizes a probe called MEPB which reacts with H2S to form excimers that emit fluorescence at 480 nm, preventing interference from thiols. This sensitive and specific quantification method has been successfully applied to track reaction of H2S with glutathione disulfide and quantify H2S production from cysteine by Escherichia coli.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Shivananda Kandagalla, Bhimanagoud Kumbar, Jurica Novak
Summary: Kyasanur Forest Disease virus (KFDV) is a neglected human pathogenic Flavivirus that causes severe hemorrhagic fever. KFDV is transmitted by the bite of hard ticks and the recent expansion of its endemic area necessitates the development of new preventive measures. Currently, there is no effective antiviral therapy or vaccine for KFDV. This study focused on the nonstructural proteins NS2B and NS3 of KFDV to identify potential allosteric sites for new drug development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ki Hyun Nam
Summary: This study investigates the structural dynamics of four loops above the substrate-binding pocket of beta-glucosidase (Bgl) enzyme. The flexibility of the loops and their role in substrate recognition were examined in Thermoanaerobacterium saccharolyticum. The findings demonstrate that the diversity in the conformation and structure of the loops contributes to the functional diversity of Bgl enzymes.
Article
Multidisciplinary Sciences
Poonam Roshan, Sahiti Kuppa, Jenna R. Mattice, Vikas Kaushik, Rahul Chadda, Nilisha Pokhrel, Brunda R. Tumala, Aparna Biswas, Brian Bothner, Edwin Antony, Sofia Origanti
Summary: Errors in chromosome segregation are associated with genomic instability in cancers. Researchers have discovered that RPA is regulated by Aurora B kinase in mitosis. Phosphorylation of Ser-384 in the DNA binding domain of RPA70 modulates chromosome segregation and genomic integrity. This study highlights the critical role of the Aurora B-RPA signaling axis in maintaining genomic stability.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Yanmin Song, Yanli Yang, Xuan Lin, Qizu Zhao, Zhiguo Su, Guanghui Ma, Songping Zhang
Summary: Size exclusion chromatography (SEC) of inactivated foot and mouth disease virus (FMDV) can induce conformational changes and decrease in immunogenicity. SEC using larger pore size media has a more significant impact on the conformation of the virus, and the conformation can be maintained by adding CaCl2 in the mobile phase.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biology
Jixue Sun, Fei Liu, Longxiao Yuan, Ning-Ning Pang, Bing Zhu, Na Yang
Summary: This study elucidates the activation mechanism of DNMT1 using various sampling methods. The results show that the binding of H3Ub2 to the RFTS domain of DNMT1 leads to conformational changes, activating DNMT1.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Chemistry, Analytical
Jing Han, Pengfei Ma, Imran Mahmood Khan, Yin Zhang, Zhouping Wang
Summary: Based on the study of the binding mechanism between antibiotic kanamycin (Kana) and aptamer, rapid fluorescent aptasensing methods were developed, and it was found that the aptamer Kmut3 had lower detection limit compared to the native aptamer.
Article
Biophysics
Daniel Dobrovodsky, Carmelo Di Primo
Summary: Surface plasmon resonance (SPR)-based biosensors are commonly used to study molecular interactions. The contribution of conformational changes to the SPR signal has been a subject of debate. This study demonstrates that conformational changes can indeed lead to a measured SPR signal.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Multidisciplinary Sciences
Patrick W. Oakes, Elizabeth Wagner, Christoph A. Brand, Dimitri Probst, Marco Linke, Ulrich S. Schwarz, Michael Glotzer, Margaret L. Gardel
NATURE COMMUNICATIONS
(2017)
Article
Biology
Kristen Witte, Devin Strickland, Michael Glotzer
Article
Cell Biology
Ingrid E. Adriaans, Angika Basant, Bas Ponsioen, Michael Glotzer, Susanne M. A. Lens
JOURNAL OF CELL BIOLOGY
(2019)
Article
Biophysics
Anindita Das, Satyaki Chatterjee, H. Raghuraman
BIOPHYSICAL JOURNAL
(2020)
Article
Biochemical Research Methods
Satyaki Chatterjee, Anindita Das, H. Raghuraman
PROTEIN EXPRESSION AND PURIFICATION
(2019)
Article
Biology
Wen Lu, Margot Lakonishok, Rong Liu, Neil Billington, Ashley Rich, Michael Glotzer, James R. Sellers, Vladimir Gelfand
Article
Biochemistry & Molecular Biology
Gargi Biswas, Semanti Ghosh, H. Raghuraman, Rahul Banerjee
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2020)
Article
Biology
Ashley Rich, Richard G. Fehon, Michael Glotzer
Article
Behavioral Sciences
Anja Richter, Mohammad Al-Bayati, Foteini Paraskevopoulou, Bernd Kraemer, Jens C. Pruessner, Elisabeth B. Binder, Oliver Gruber
Summary: The psychosocial stress effects of urban living are associated with increased risk for schizophrenia, mood and anxiety disorders due to alterations in stress-induced activity in the amygdala and pregenual anterior cingulate cortex. Genetic factors, such as FKBP5, may modulate the impact of city living on stress processing. The interaction between city living and genetic variation in FKBP5 (rs3800373) was found to modulate responses in the subgenual and pregenual ACC, potentially increasing the risk for developing stress-related mental disorders in city dwellers carrying the FKBP5 minor risk allele.
STRESS-THE INTERNATIONAL JOURNAL ON THE BIOLOGY OF STRESS
(2021)
Article
Biochemistry & Molecular Biology
Anindita Das, H. Raghuraman
Summary: The study demonstrates that the surface charge of the membrane does not significantly affect the topology and structural dynamics of the sensor loop in KvAP-VSD, while the dynamic variability of the sensor loop is preserved in both zwitterionic and anionic membranes. Furthermore, the lifetime distribution peaks of the sensor loop are broadened in membranes compared to micelles, indicating an altered conformational heterogeneity of the sensor loop in membrane environments.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Biochemistry & Molecular Biology
Anindita Das, Arpan Bysack, H. Raghuraman
Summary: The dual-detergent strategy using inexpensive detergents has been shown to be highly effective in purifying different classes of membrane proteins in a cost-effective manner.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Rupasree Brahma, H. Raghuraman
Summary: This review discusses the widely used methods for accurately determining the membrane penetration depths of fluorescent probes and also introduces a novel fluorescence quenching method. These methods are important and applicable for studying membrane proteins.
JOURNAL OF MEMBRANE BIOLOGY
(2022)
Article
Biology
Katrina M. Longhini, Michael Glotzer
Summary: In the early Caenorhabditis elegans embryo, cell polarization and cytokinesis are closely related but distinct processes. This study reveals that polar relaxation is associated with the depletion of the RhoGEF protein ECT-2 at the posterior cortical region. Additionally, centrosome integrity, Aurora A, and myosin-dependent cortical flows are required for the asymmetric accumulation of ECT-2. The phosphorylation of ECT-2 by centrosomal AIR-1 breaks symmetry and is further amplified by myosin-driven flows, leading to localized inhibition of ECT-2. These mechanisms together contribute to the polarized assembly of cortical myosin and play important roles in embryo polarization and cytokinesis.
Review
Biochemistry & Molecular Biology
Rupasree Brahma, H. Raghuraman
Summary: Protein hydration dynamics are crucial in physiological processes, and the unique REES fluorescence method can directly monitor environmental restrictions and dynamics around a polar fluorophore. The review focuses on recent applications and novel data analysis of REES, as well as discussing its utility in imaging protein aggregates in a cellular context. The potential of REES approach showcased in this review is believed to attract more researchers, particularly from the life sciences field.
EMERGING TOPICS IN LIFE SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
H. Raghuraman, Satyaki Chatterjee, Anindita Das
FRONTIERS IN MOLECULAR BIOSCIENCES
(2019)