Article
Multidisciplinary Sciences
Rajkama, Nisal, P. Jitendra, Agata, Susan, Geoff, W. Aaron, J. Anita, Namita Roy, K. Naba
Summary: This study reveals the impact of crowding on the dynamic conformation of intrinsically disordered proteins (IDPs). Through experimental methods and model construction, researchers found that crowding can induce specific conformational changes in IDPs. This study is of great importance for a better understanding of the interactions and structural dynamics of IDPs in crowded environments.
Article
Chemistry, Physical
Pablo M. Blanco, Sergio Madurga, Josep L. Garces, Francesc Mas, Rita S. Dias
Summary: This study investigates the coupling between ionization and conformational properties of two intrinsically disordered proteins in the presence of neutral and charged crowders, revealing different charge regulation mechanisms under different conditions.
Article
Biochemistry & Molecular Biology
Tobias Gruber, Marc Lewitzky, Lisa Machner, Ulrich Weininger, Stephan M. Feller, Jochen Balbach
Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure elements and play important roles in cellular processes. This study focuses on the C-terminal region of Gab1, an IDP, and investigates its induced structure and binding properties under both non-crowding and crowding conditions. The results show that under crowding conditions, pre-structured motifs are formed in certain regions of Gab1, which are also the binding regions for the protein SHP2. Phosphorylation has no impact on the dynamics and disordered nature of Gab1. Therefore, biological crowders can enhance the binding capacity of SHP2 to Gab1, even in the absence of phosphorylation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Samuel Naudi-Fabra, Maud Tengo, Malene Ringkjobing Jensen, Martin Blackledge, Sigrid Milles
Summary: Studying the conformational landscape of intrinsically disordered and partially folded proteins is challenging and requires an integrated approach using multiple techniques to accurately describe the conformational ensembles of these proteins. This integrated approach has been successfully tested and validated, providing new insights into the conformational landscape of viral proteins and demonstrating its potential for integrative dynamic structural biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Akihisa Miyagawa, Hiroyuki Komatsu, Shigenori Nagatomo, Kiyoharu Nakatani
Summary: This study investigates the thermodynamic behavior of acid dissociation of 8-hydroxyquinolin-5-sulfonic acid in a molecular crowding environment and finds that it is influenced by the presence of polyethylene glycol (PEG), which leads to dehydration of the dissociated species, explaining the process of acid dissociation.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Tasneem Ottallah, Sophia A. Parandian, Steven W. Rick
Summary: Two different potentials, the modified TraPPE-UA model and the modified GAFF model, are tested for temperature-dependent properties of PEO, with the TraPPE-UA model found to be more accurate in reproducing experimental properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Neha Raina, Sheeza Khan, Ranjani Soundhararajan, Mohammad Shahid, Hemalatha Srinivasan, Asimul Islam
Summary: The interactions between nano colloids synthesized from Cymbopogon citratus extract and holo alpha-lactalbumin (h-alpha-LA) were investigated in this study. The results showed significant perturbations in the protein's structure and stability in the presence of nano colloid. This study provides important insights for the development of nano colloid-based products for human use.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Jung Min Kim, Baik Lin Seong, Jinho Jung
Summary: This study developed a method to label intrinsically disordered native proteins (IDNPs) in mammalian cells while preserving their active structures. By using pure fluorescent methionine and ATTO 565-biotin, IDNPs were labeled at the N- or C-terminus and their concentrations were detected using Ni-NTA beads. The study also demonstrated double labeling of genetically encoded fluorescent-Tat expression using a single fluorescent dye pair and FRET ratio and two-color correlation analysis. This research aims to address native protein processing and achieve ultrasensitive protein folding for nanoscale biological and ecological applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Neha Raina, Md. Imtaiyaz Hassan, Faizan Ahmad, Asimul Islam, Amit Kumar Singh
Summary: Crowding and confinement in macromolecular environments can affect protein stability through a balance of hard-core repulsion and chemical interactions. Past studies have shown the impact of PEG on proteins, with destabilizing interactions potentially caused by excluded volume effects or changes in solvent properties. Charge-charge and hydrophobic interactions play a significant role in destabilizing protein interactions, particularly in the presence of crowding agents like proteins.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemical Research Methods
Lei Yu, Rafael Bruschweiler
Summary: The article investigates the molecular simulation of two intrinsically disordered proteins (IDPs) and validates them with experimental data. The results show that the new molecular dynamics simulation method can generate highly realistic protein conformational ensembles, which are of great significance for understanding the biological function of IDPs.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Energy & Fuels
Mengman Weng, Jingtao Su, Jiahui Lin, Jintao Huang, Yonggang Min
Summary: Green energy conversion and storage materials are currently receiving research attention. This study focuses on a framework material composed of polyaniline (PANI) and MXene, which exhibits strong light absorption and excellent cycling stability for solar-light thermal energy conversion. Composite phase change materials prepared using polyethylene glycol (PEG) and PANI/MXene show great reusable capacity for solar light response and thermal energy storage. Among the composites, PM24 (n(PANI): n(MXene) = 100:24) shows the best comprehensive performance with high latent heat values, high enthalpy efficiency, and superior cycling stability. With high solar-to-thermal conversion efficiency exceeding 95.29%, PM24 has significant potential for long-term heat storage and photothermal conversion.
SOLAR ENERGY MATERIALS AND SOLAR CELLS
(2023)
Article
Chemistry, Multidisciplinary
Hiromitsu Shimoyama, Yasushige Yonezawa
Summary: In this study, a novel multi-scale divide-and-conquer MD (MSDC-MD) method was proposed to speed up the conformation sampling of the intrinsically disordered region (IDR) of calcineurin. By combining all atom model (AAM) molecular dynamics (MD) with coarse-grained model MD (CGM-MD), the MSDC-MD approach first samples wide conformation space using CGM before initiating multiple AAM-MD simulations in a limited area. The performance was evaluated by sampling the ordered conformation of the IDR, resulting in a root-mean-square distance (RMSD) of 2.23 angstrom with respect to the experimental structure.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Madison. A. A. Stringer, Jasmine Cubuk, J. Jeremias Incicco, Debjit Roy, Kathleen. B. B. Hall, Melissa. D. D. Stuchell-Brereton, Andrea Soranno
Summary: The crowded cellular environment has an impact on protein conformations, dynamics, and interactions, particularly on intrinsically disordered proteins and regions. This study investigates the effect of crowding using polyethylene glycol (PEG) on the intrinsically disordered tail of the SARS-CoV-2 nucleocapsid protein. It is found that high-molecular-weight PEG leads to the collapse of the disordered tail, while low-molecular-weight PEG causes chain expansion. The study also explores the interaction between the protein and RNA in the presence of crowding agents, revealing the role of nonspecific protein-PEG interactions and entropic effects.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Review
Chemistry, Multidisciplinary
Jasmine Cubuk, Andrea Soranno
Summary: This article discusses the effects of cellular environment on intrinsically disordered proteins. Unlike structured proteins, intrinsically disordered proteins do not have a stable three-dimensional structure and remain flexible and dynamic in solution. The physics of polymers and colloids provides a framework to interpret how crowding affects the conformation, dynamics, and interactions of disordered proteins.
Article
Plant Sciences
Alexander Kartashov, Ilya E. Zlobin, Pavel P. Pashkovskiy, Elena S. Pojidaeva, Yury Ivanov, Anna S. Mamaeva, Igor A. Fesenko, Vladimir V. Kuznetsov
Summary: Dehydrins are important components of plant stress tolerance, with a large gene family in conifers implicated in physiological functions. The study focused on dehydrin regulation in Scots pine and Norway spruce seedlings under osmotic stress, revealing the constitutive physiological functions of AESK-type dehydrins in Pinaceae plants. The expression of dehydrin genes in response to stress showed significant changes, with low basal expression genes demonstrating the most prominent changes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Chemistry, Physical
Huan-Xiang Zhou
Summary: Biomolecular condensates exhibit viscoelastic properties that can be captured by a simple model, with modulation of intermolecular interactions affecting the components differently. The tendency of condensates to fuse is influenced by interfacial tension and viscosity, with shear relaxation dynamics playing a role in fusion speed. These insights contribute to bridging the gap between the biology and physics of biomolecular condensates.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yuqin Yang, Hao Dong, Huan-Xiang Zhou
Summary: The study found that cholesterol has a significant impact on the distribution of the anti-influenza drug amantadine in bilayers, with cholesterol reducing the amount of amantadine in the membrane mainly by perturbing the bilayer structure and dynamics. Surrounding lipids stabilize amantadine by wrapping their tails around the drug molecule, a function compromised in the presence of cholesterol due to increased lipid tail order.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Xu Dong, Ling-Yun Qin, Zhou Gong, Sanbo Qin, Huan-Xiang Zhou, Chun Tang
Summary: Nonspecific binding of crowder proteins with functional proteins is common in vivo, with bovine serum albumin weakly but preferentially interacting with the histidine carrier protein (HPr). This competition with HPr's specific partner protein, EIN, decreases the binding affinity and accelerates dissociation of the native complex, while Ficoll-70 stabilizes the complex and slows dissociation. Atomistic modeling of macromolecular crowding rationalizes the experimental data and provides insights into protein-crowder interactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Konstantinos Mazarakos, Huan-Xiang Zhou
Summary: In this study, a mean-field theoretical model and molecular dynamics simulations are used to demonstrate that the multiphase organization of multi-component condensates undergoes a second phase transition, driven by the difference in attraction strengths between different components. The phase transitions are observed by decreasing the temperature, leading to condensate separation from the bulk phase and component demixing within the condensates. Molecular dynamics simulations of model mixtures verify the existence of a critical temperature for demixing and predicted binodals.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Divya Kota, Huan-Xiang Zhou
Summary: This study found that macromolecular regulators have effects on the material properties of biomolecular condensates, including phase equilibrium, interfacial tension, viscoelasticity, fusion speed, etc. These results illustrate the opportunities for tuning material properties.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biology
Aayush Gupta, Souvik Dey, Alan Hicks, Huan-Xiang Zhou
Summary: This study developed generative autoencoders that can learn from short molecular dynamics simulations and generate full conformational ensembles of intrinsically disordered proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sanbo Qin, Alan Hicks, Souvik Dey, Ramesh Prasad, Huan-Xiang Zhou
Summary: This study identified the membrane-association characteristics of intrinsically disordered regions (IDRs) in proteins and developed a web server called ReSMAP for predicting residue-specific membrane-association propensities from IDR sequences.
Article
Chemistry, Physical
Souvik Dey, Matthew MacAinsh, Huan-Xiang Zhou
Summary: For intrinsically disordered proteins (IDPs), the dynamics of the backbone play a key role in encoding their function. The dynamics are regulated by local interactions, secondary structures, and glycines. These sequence-dependent changes in backbone dynamics allow IDPs to respond to binding partners in a versatile manner.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Konstantinos Mazarakos, Ramesh Prasad, Huan-Xiang Zhou
Summary: Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes. However, there is still a difficulty in computing the binodal from molecular dynamics simulations of IDPs. In this study, a new method called SpiDec is proposed, which allows for the accurate determination of the phase equilibrium of IDPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Matthew MacAinsh, Huan-Xiang Zhou
Summary: Tau, an intrinsically disordered protein, binds to both microtubules and acidic membranes. This study used molecular dynamics simulations to investigate the dynamic binding of Tau to an acidic membrane. The simulations validated the interaction between amphipathic helices in Tau and the membrane, and showed similarities and differences in residue contacts between Tau and microtubules. This mimicry facilitates both the anchoring of microtubules to membranes and the transfer of Tau from membranes to microtubules.
Article
Chemistry, Physical
Huan-Xiang Zhou
Summary: This article introduces an approach for estimating the lower and upper bounds of sample data using O(N) operations. The approach calculates the mean values of the smallest and largest x values in N-point samples and fits them as functions of N to obtain the estimates for the bounds. Application to synthetic data demonstrates the accuracy and reliability of this approach.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Souvik Dey, Huan-Xiang Zhou
Summary: This study used molecular dynamics simulations to investigate the regulation of the IDP N-WASP, finding that intramolecular interactions keep N-WASP in an autoinhibited state and PIP2 binding can activate it by freeing the acidic motif, which interacts with Arp2/3 to initiate actin polymerization. Competition exists between PIP2 and the acidic motif for binding to the basic region. Even at a 30% PIP2 level in the membrane, the acidic motif only contacts the basic region in 8.5% of the population.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Johansen B. Amin, Miaomiao He, Ramesh Prasad, Xiaoling Leng, Huan-Xiang Zhou, Lonnie P. Wollmuth
Summary: NMDA receptors have two gates that are regulated by distinct subunits, with one gate mainly regulating single channel events and the other gate mainly regulating entry and exit from clusters. The unique kinetics of NMDARs contribute to their role in synaptic signaling, with clusters of rapid opening and closing separated by long silent periods.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Sean T. Smrt, Cristian A. Escobar, Souvik Dey, Timothy A. Cross, Huan-Xiang Zhou
Summary: Mtb infects a quarter of the worldwide population and the rising drug resistance makes it urgent to better understand Mtb cell division. The study reveals that the transmembrane protein FtsQ may serve as a membrane anchor of the Mtb Z-ring, and its disordered cytoplasmic region interacts with multiple partners, indicating its potential role in cell division and as a drug target.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Guodong Hu, Huan-Xiang Zhou
Summary: The SAM/SAH riboswitch binds SAM and SAH with similar affinities. Molecular dynamics simulations reveal the role of Mg2+ ions in stabilizing the RNA structure, widening the groove for ligand entry, and facilitating ribosome binding. Mg2+ plays vital roles in the function of the SAM/SAH riboswitch.
COMMUNICATIONS BIOLOGY
(2023)