Article
Biotechnology & Applied Microbiology
Taolan Zhao, Yan-Ming Chen, Yu Li, Jia Wang, Siyu Chen, Ning Gao, Wenfeng Qian
Summary: The study revealed widespread ribosome collisions in cells, which are associated with slow ribosome release, slow peptide bond formation, and slow leaving of polylysine from the exit tunnel of ribosomes. Collisions occur more frequently in the gap regions between alpha-helices, where translational pauses can prevent interference with protein folding by downstream peptides. Paused or collided ribosomes are associated with specific chaperones, facilitating proper protein folding during translation.
Article
Biology
Mihaly Badonyi, Joseph A. Marsh, Marina Rodnina
Summary: Recent evidence suggests that cotranslational assembly of protein complexes is particularly common between subunits that form large intermolecular interfaces. This study provides further support for this notion and demonstrates that large interfaces have evolved to maximize the chance of successful cotranslational subunit binding.
Article
Multidisciplinary Sciences
Evan Mercier, Xiaolin Wang, Manisankar Maiti, Wolfgang Wintermeyer, Marina Rodnina
Summary: The study reveals that during the synthesis of membrane proteins, the lateral gate fluctuations are highly dynamic, continuously sampling between open and closed states even without ligands. Ribosome binding and transmembrane segment insertion do not stop the gate fluctuations but tend to increase sampling of the open state. Binding of YidC facilitates substantial opening of the gate, aiding in the folding of YidC-dependent polytopic membrane proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Migle Kisonaite, Klemens Wild, Karine Lapouge, Genis Valentin Gese, Nikola Kellner, Ed Hurt, Irmgard Sinning
Summary: The authors used cryo-EM to investigate how the RAC complex, a conserved ribosome-associated chaperone triad, assists in cotranslational protein folding. They determined cryo-EM structures of RAC bound to 80S ribosomes, revealing two distinct conformations and a tight interaction between the RAC components. They also discovered a non-canonical interaction that masks the HPD motif in the J domain protein Zuo1, allowing proper positioning of Ssb for activation. These findings provide insights into the dynamic interaction and protein folding process involving RAC and Ssb.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Hao-Hsuan Hsieh, Shu-ou Shan
Summary: The fidelity of protein targeting is crucial for proper organelle functioning. The mechanisms by which cells achieve high accuracy in protein localization are not fully understood. This chapter reviews recent progress in understanding the molecular mechanisms and substrate selection of the SRP pathway in mammals, with a focus on the role of the cotranslational chaperone NAC in protein localization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ruiyue Tan, Margaret Hoare, Kevin A. Welle, Kyle Swovick, Jennifer R. Hryhorenko, Sina Ghaemmaghami
Summary: The folding of proteins during translation while bound to the ribosome is not well understood. This study developed a method using mass spectrometry to measure the stability of nascent polypeptide chains. The results showed that the ribosome significantly influences the stability of the nascent polypeptides, with variations depending on different folding domains and localized charge distributions within the polypeptides. The study suggests that electrostatic interactions between the ribosome and nascent polypeptides play a role in these stability modulations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Zikun Zhu, Shuai Wang, Shu-ou Shan
Summary: Using ribosome profiling methods, this study elucidates the cotranslational interaction principles of SecA with nascent proteins and reveals a hierarchical organization of protein export pathways in bacteria.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ying Zhang, Evelina De Laurentiis, Katherine E. Bohnsack, Mascha Wahlig, Namit Ranjan, Simon Gruseck, Philipp Hackert, Tina Wolfle, Marina Rodnina, Blanche Schwappach, Sabine Rospert
Summary: The GET pathway aids in delivering tail-anchored proteins to the ER, with Get4/5 components probing near the ribosomal exit tunnel and recruiting Sgt2 upon emergence of client proteins to initiate the targeting phase of the pathway.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Ronaldo Junio de Oliveira
Summary: The computer-designed Top7 scaffold was used to produce immunoreactive proteins by grafting the 2F5 HIV-1 antibody epitope, which effectively induced and detected HIV-1 antibodies. However, protein aggregation was observed in the grafted Top7-2F5 design, while the soluble biotinylated Top7-2F5-biotin did not have this issue. The study predicted an increase in thermodynamic cooperativity of Top7 after grafting and biotin-labeling, reducing intermediate state populations. Investigating folding kinetic traps and coordinate-dependent coefficients may be useful in predicting aggregated kinetic traps of scaffold-epitope proteins for novel diagnostic and therapeutic platforms.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Michal H. Kolar
Summary: Proteins, composed of amino acids, play essential roles in virtually all biological processes. Synthesized on ribosomes through a process called translation, proteins spend a significant amount of time attached to the ribosome. This review focuses on events involving nascent proteins during their synthesis, co-translationally, shedding light on the initial moments of protein formation.
Article
Chemistry, Multidisciplinary
Elke De Zitter, Siewert Hugelier, Sam Duwe, Wim Vandenberg, Alison G. Tebo, Luc Van Meervelt, Peter Dedecker
Summary: Anisotropic environments can significantly impact the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. By studying fluorescent proteins as model systems, it was found that changes in spectroscopic properties can be attributed to multiple underlying mechanisms. The research highlights the complex interplay between structure and spectroscopy, identifying key modulators like polarity, hydrogen bonding, and presence of water molecules.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Robin Ganesan, Kotchaphorn Mangkalaphiban, Richard E. E. Baker, Feng He, Allan Jacobson
Summary: This study reveals that Upf1, Upf2, and Upf3 are essential regulators of nonsense-mediated mRNA decay (NMD). They exert their NMD functions while bound to elongating ribosomes. The findings also shed light on the timing and specificity of Upf1 association with translating ribosomes, as well as its impact on translation termination and ribosome release.
Article
Microbiology
Kilian Schumacher, Rick Gelhausen, Willow Kion-Crosby, Lars Barquist, Rolf Backofen, Kirsten Jung
Summary: This study compared the response of E.coli to different levels of acid stress using ribosome profiling and RNA sequencing. New genes and pathways were identified, and machine learning was utilized to distinguish the response to acid stress from general stress.
Article
Multidisciplinary Sciences
You Yu, Shibai Li, Zheng Ser, Huihui Kuang, Thane Than, Danying Guan, Xiaolan Zhao, Dinshaw J. Patel
Summary: In this study, the cryo-EM structure of DNA-bound Saccharomyces cerevisiae Smc5/6 complex was determined, revealing intricate interactions among core subunits and the mechanism of DNA binding. The Smc5/6 complex was found to form a clamp that encircles the DNA, with multiple subunits binding to DNA in a nonsequence-specific manner. These findings are significant for our understanding of the importance of SMC complexes in maintaining chromatin organization and function throughout the cell cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Mathew McLaren, Rebecca Conners, Michail N. Isupov, Patricia Gil-Diez, Lavinia Gambelli, Vicki A. M. Gold, Andreas Walter, Sean R. Connell, Bryony Williams, Bertram Daum
Summary: Translational control is a crucial process for cells to adapt to changing conditions. This study investigated the hibernating ribosomes in microsporidian parasites and revealed their unique dimerization mechanism. The findings provide structural evidence for ribosomal hibernation and demonstrate the utilization of dimerization in translational control by eukaryotes.
NATURE MICROBIOLOGY
(2023)
Article
Biophysics
Amitabha Chattopadhyay, Satinder S. Rawat, Denise V. Greathouse, Devaki A. Kelkar, Roger E. Koeppe
BIOPHYSICAL JOURNAL
(2008)
Article
Biophysics
Devaki A. Kelkar, Arunima Chaudhuri, Sourav Haldar, Amitabha Chattopadhyay
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2010)
Article
Genetics & Heredity
Casper Groth, Pooja Vaid, Aditi Khatpe, Nelchi Prashali, Avantika Ahiya, Diana Andrejeva, Madhumita Chakladar, Sanket Nagarkar, Rachel Paul, Devaki Kelkar, Teresa Eichenlaub, Hector Herranz, T. S. Sridhar, Stephen M. Cohen, L. S. Shashidhara
G3-GENES GENOMES GENETICS
(2020)
Review
Oncology
Apurv Kulkarni, Devaki A. Kelkar, Nidhi Parikh, Lingadahalli S. Shashidhara, Chaitanyanand B. Koppiker, Madhura Kulkarni
JCO GLOBAL ONCOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Devaki A. Kelkar, Amitabha Chattopadhyay
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2007)
Review
Biochemistry & Molecular Biology
Abhijit Chakrabarti, Devaki A. Kelkar, Amitabha Chattopadhyay
BIOSCIENCE REPORTS
(2006)
Article
Biochemistry & Molecular Biology
DA Kelkar, A Chattopadhyay
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2006)
Article
Biophysics
A Chattopadhyay, A Arora, DA Kelkar
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2005)
Article
Biophysics
SS Rawat, DA Kelkar, A Chattopadhyay
BIOPHYSICAL JOURNAL
(2005)
Article
Biochemistry & Molecular Biology
DA Kelkar, A Chattopadhyay, A Chakrabarti, M Bhattacharyya
Article
Biophysics
DA Kelkar, A Chattopadhyay
BIOPHYSICAL JOURNAL
(2005)
Article
Chemistry, Physical
DA Kelkar, A Chattopadhyay
JOURNAL OF PHYSICAL CHEMISTRY B
(2004)
Review
Biochemistry & Molecular Biology
Devaki A. Kelkar, Amitabha Chattopadhyay
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2007)
Editorial Material
Biology
Devaki A. Kelkar, Amitabha Chattopadhyay
JOURNAL OF BIOSCIENCES
(2006)