Article
Chemistry, Multidisciplinary
Anirban Das, Anju Yadav, Mona Gupta, R. Purushotham, Vishram L. Terse, Vicky Vishvakarma, Sameer Singh, Tathagata Nandi, Arkadeep Banerjee, Kalyaneswar Mandal, Shachi Gosavi, Ranabir Das, Sri Rama Koti Ainavarapu, Sudipta Maiti
Summary: By constructing a xenonucleus based on specific design principles, the refolding speed of ubiquitin protein can be increased. This method provides a new approach for constructing specific folding catalysts for proteins with well-defined folding nuclei.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Surabhi Mehra, Sahil Ahlawat, Harish Kumar, Debalina Datta, Ambuja Navalkar, Nitu Singh, Komal Patel, Laxmikant Gadhe, Pradeep Kadu, Rakesh Kumar, Narendra N. Jha, Arunima Sakunthala, Ajay S. Sawner, Ranjith Padinhateeri, Jayant B. Udgaonkar, Vipin Agarwal, Samir K. Maji
Summary: This study demonstrates the structure-function relationship of two polymorphs (PMFs and HMFs) based on alpha-Syn aggregation intermediates. These polymorphs show distinct structural differences and cellular activities, which have important implications for the occurrence and propagation of synucleinopathies.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Genetics & Heredity
Gongwang Yu, Hanbing Zhu, Xiaoshu Chen, Jian-Rong Yang
Summary: The study investigates the secondary structure characteristics of mRNAs and their importance in function and evolution. It is found that specific folding of mRNAs may be an adaptive trait associated with important genes or sites, potentially providing the advantage of modulating ribosome movement. This reveals a novel aspect of the RNA structurome with functional and evolutionary implications.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Edward A. Dennis
Summary: Lipids play important roles in chronic diseases, but defining the substrate specificity of lipid metabolism enzymes is challenging. This research focuses on how membranes interact with enzymes to regulate cell signaling and metabolic pathways. By using substrate lipidomics and molecular dynamics simulations, the study reveals the link between enzyme specificity and hydrophobic binding subsites for membrane phospholipid substrates.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yeganeh Habibi, Nuwani W. Weerasinghe, Kevin A. Uggowitzer, Christopher J. Thibodeaux
Summary: This study investigates the structure relationship between lanthipeptide synthetases and their precursor peptides using mass spectrometry. The results show that post-translational modifications of the precursor peptide can change the conformational dynamics of the synthetase and provide a mechanistic model for this process.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Rachel E. Wilkinson, Katelyn N. Kraichely, Cecilia M. Hendy, Lauren E. Buchanan, Stuart Parnham, Michael W. Giuliano
Summary: This study presents the NMR solution structure of full-length human galanin C-terminal amide, revealing an irregular helical structure at its N-terminus and flexibility in the C-terminus, which plays a role in pre-organizing the galanin receptor binding epitope. The findings provide new insights into the function of galanin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Zengqi Lu, Xiaolong Fu, Jingwei Hou, Lei Yue, Jiamao Li, Guangming Ran, Chengjian Xiao, Xiaolin Wang
Summary: To enhance hydrogen-water isotope exchange performance, a hydrophobic microenvironment was created within the catalyst support and a bimetal catalyst was utilized. The superhydrophobic catalyst exhibited significant improvement in performance. Adsorption/desorption tests demonstrated that the hydrophobic microenvironment increased the diffusion rate of reactants, while metal doping modification enhanced reactant concentration around the active site. Overall, the catalytic performance of the catalyst with the hydrophobic microenvironment exceeded that of normal hydrophobic catalysts, even with slightly diminished hydrophobicity.
CATALYSIS COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Rupam Bhattacharjee, Jayant B. B. Udgaonkar
Summary: Distinguishing competing pathways of protein folding based on the differences in their progress of structure acquisition is a challenge in protein folding studies. This study used pulsed hydrogen exchange labeling methodology with mass spectrometry to characterize the folding of a heterodimeric protein, double chain monellin (dcMN). The folding mechanism of dcMN was described as a triangular three-state mechanism, and the alternative folding pathways were differentiated based on the progress of structure acquisition. The intermediates on the pathways showed differences in the acquisition of protective structure, particularly in the beta 2 region.
Article
Biochemistry & Molecular Biology
Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
Summary: The study demonstrates that the residue folding degree-based collective variable can track the evolution of secondary structures in protein dynamics, providing insight into the energy profiles and transition barriers during protein folding process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Vo Hong Thanh, Dani Korpela, Pekka Orponen
Summary: The study proposes a kinetic model for RNA folding process that takes into account cotranscriptional effects, which can predict favored conformations in actual biological systems. The computational tool developed in the study offers valuable insights into the kinetics of RNA folding.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Rohit Jain, Khaja Muneeruddin, Jeremy Anderson, Michael J. Harms, Scott A. Shaffer, C. Robert Matthews
Summary: The study revealed the folding mechanisms of bacterial IGPS TIM barrel enzyme using HDX-MS, identifying protected sites and stable cores, and emphasizing the key role of hydrophobicity in stabilizing high-energy folding intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Ilia Korobko, Robin Benjamin Eberle, Mousam Roy, Amnon Horovitz
Summary: This study shows that the stability of protein substrates in the GroEL/ES chaperonin cage is dramatically reduced, partially due to a diminished hydrophobic effect. The reduced hydrophobic effect is likely caused by water ordering due to a small number of hydration shells between the cavity and protein substrate surfaces.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Hiram Isaac Beltran, Salomon J. Alas-Guardado, Pedro Pablo Gonzalez-Perez
Summary: In this study, the folding of 7 hydrophobic-polar sequences in two types of 2D-square space lattices, homogeneous and correlated, was tested. It was found that using correlated networks led to more successful structural trials compared to a homogeneous lattice. The majority of the sequences were designed by the researchers, and the goal of the study was to obtain a modified 2D HP lattice model that mimics protein folding in crowded environments. The results showed that folding sequences in crowded spaces achieved better results than in homogeneous ones.
JOURNAL OF MOLECULAR MODELING
(2022)
Review
Biochemistry & Molecular Biology
Chiaki Nishimura, Takeshi Kikuchi
Summary: Protein folding is crucial for its proper function, and this review focuses on the formation of helical structures in globin proteins and the occurrence of non-native and misfolded structures. The research presented aims to characterize the intermediates and the complete folding pathway to understand the mechanisms of misfolding and the role of non-native structures in the folding intermediate. The article also discusses the stabilization and slower folding induced by non-native structures.
Article
Biochemistry & Molecular Biology
Fengfei Wang, Wei Li, Baiyi Li, Liangxu Xie, Yunguang Tong, Xiaojun Xu
Summary: Circular RNAs (circRNAs) are a unique type of non-coding RNA that form a closed loop structure without ends. They have important biological roles and potential applications in clinical and research fields. The cRNAsp12 server predicts the secondary structures and folding stabilities of circRNAs, providing users with various options for structure predictions and customization of constraints.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)