Article
Multidisciplinary Sciences
Marco Janoschke, Mirjam Zimmermann, Anna Brunauer, Raffael Humbel, Tina Junne, Martin Spiess
Summary: The topology of membrane proteins is defined by the integration of alpha-helical transmembrane domains at the Sec61 translocon. Different sequences preceding a potential transmembrane domain significantly affect the hydrophobicity requirement for integration, with rapidly folding domains and strong chaperone binding facilitating efficient transmembrane integration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Lukas Rohland, Roman Kityk, Luka Smalinskaite, Matthias P. Mayer
Summary: The 70 kDa heat shock proteins (Hsp70s) are versatile molecular chaperones that assist in protein-folding processes. ATP and cochaperones induce structural rearrangements in Hsp70, with peptides causing larger changes and protein clients being more effective in stimulating ATP hydrolysis. The study provides insights into the mechanics, allostery, and dynamics of Hsp70 chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Huafeng Xu
Summary: Recent experimental studies have shown that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. This article proposes a unifying principle based on available evidence, which explains the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation.
Article
Multidisciplinary Sciences
Jonathan J. Knowlton, Daniel Gestaut, Boxue Ma, Gwen Taylor, Alpay Burak Seven, Alexander Leitner, Gregory J. Wilson, Sreejesh Shanker, Nathan A. Yates, B. V. Venkataram Prasad, Ruedi Aebersold, Wah Chiu, Judith Frydman, Terence S. Dermody
Summary: The TRiC chaperonin plays a crucial role in folding and assembly of the reovirus sigma 3 capsid protein, interacting with a network of chaperones including prefoldin. This study sheds light on the molecular dynamics of sigma 3 folding and establishes a biological function for TRiC in virus assembly, while also providing structural and functional insights into how TRiC and prefoldin participate in protein complex assembly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Il-Soo Park, Seongchan Kim, Yeajee Yim, Ginam Park, Jinahn Choi, Cheolhee Won, Dal-Hee Min
Summary: This study reports the creation of a synthetic chaperone to control the folding of therapeutic peptides and demonstrates its enhanced therapeutic potential in a tumor model. The synthetic chaperone, based on porous nanoparticles, provides an internal hydrophobic environment which stabilizes the secondary structure of the encapsulated peptides. Additionally, the modified nanoparticles serve as a nanoreactor and effectively deliver the stabilized peptides into cancer cells, resulting in inhibition of cancer growth.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Philip To, Yingzi Xia, Sea On Lee, Taylor Devlin, Karen G. Fleming, Stephen D. Fried
Summary: The process of protein folding is complex and important, involving cellular factors and processes. Researchers have developed a new method to monitor the structural changes of Escherichia coli proteins in the cell cytosol and with chaperones. The results show that GroEL can assist in refolding the majority of proteins, while DnaK and GroEL have a similar set of proteins that they refold. Additionally, some proteins are not able to be refolded with any chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Filipe E. P. Rodrigues, Antonio J. Figueira, Claudio M. Gomes, Miguel Machuqueiro
Summary: Computational analysis revealed that Aβ-Lys28 plays a key role in stabilizing interactions with S100B, involving residues such as Met79, Thr82, and Glu86. Coulombic interactions, potentially involving the Lys28(Aβ)/Glu86(S100B) pair, are crucial for the holdase-type chaperone activity of S100B, and high ionic strength can reduce the anti-aggregation activity of the Aβ-S100B interaction through electrostatic perturbation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Rafayel Petrosyan, Abhishek Narayan, Michael T. Woodside
Summary: Single-molecule force spectroscopy (SMFS) is a powerful tool for studying protein folding dynamics, uncovering energy landscapes of folding, complex folding pathways, mechanisms of chaperones in assisting folding, effects of ribosomes on co-translational folding, and monitoring membrane protein folding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Awa Diop, Daniele Santorelli, Francesca Malagrino, Caterina Nardella, Valeria Pennacchietti, Livia Pagano, Lucia Marcocci, Paola Pietrangeli, Stefano Gianni, Angelo Toto
Summary: This review summarizes the latest research on the structure, function, pathogenic role, and regulation of SH2 domains. The findings suggest that pharmacological interest in SH2 domains and a deeper understanding of their binding properties are crucial.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Harsimranjit Sekhon, Jeung-Hoi Ha, Stewart N. Loh
Summary: Protein conformational switches can be constructed by fusing an input domain that recognizes a target ligand to an output domain that establishes a biological response. This study successfully converted the ribonuclease barnase to a switchable enzyme by duplicating a portion of its sequence and adding FK506 binding protein copies, resulting in complementary folding events that activate the enzyme's function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Immunology
Xizhen Zhang, Wei Yu
Summary: Heat shock proteins (HSPs) are proteins found in bacterial, plant, and animal cells that play a role in regulating cellular activities. They protect other proteins under stress by controlling protein folding and maintaining their correct structure. Some HSPs have antiviral effects during viral infection by activating immune pathways. However, viruses can also exploit HSPs to aid their invasion and replication. This review summarizes the roles of HSPs in viral infection and their potential use in antiviral therapy.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Stella Prins, Valentina Corradi, David N. N. Sheppard, D. Peter Tieleman, Paola Vergani
Summary: Deletion of phenylalanine 508 (F508del) in the cystic fibrosis transmembrane conductance regulator (CFTR) protein has a significant impact on membrane proximity and ion-channel function. Mutagenesis scan of intracellular loop 4 (ICL4) reveals that second-site mutations, such as R1070W, F1068M, and F1074M, can partially rescue F508del defects. Molecular dynamics simulations highlight the importance of flexibility and aromatic sidechains at the ICL4/NBD1 interface in F508del-induced dysfunction.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Biophysics
Judy L. M. Kotler, Timothy O. Street
Summary: The Hsp40, Hsp70, and Hsp90 chaperone families play important roles in cellular protein homeostasis. Recent studies have explored the possibility of understanding how these chaperones work together as a unified system. This review focuses on the mechanics of ERdj3 (an Hsp40), BiP (an Hsp70), and Grp94 (an Hsp90) chaperones within the endoplasmic reticulum, examining their interactions and the gaps in our understanding. Calculations are also used to investigate the impacts of client transfer on protein solubilization, protein folding, and triage decisions for protein degradation. Experimental tests of the proposed roles of client transfer among Hsp40-Hsp70-Hsp90 chaperones are discussed.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Developmental Biology
Makoto Abe, Timothy C. Cox, Anthony B. Firulli, Stanley M. Kanai, Jacob Dahlka, Kim-Chew Lim, James Douglas Engel, David E. Clouthier
Summary: Neural crest cells in the mandibular and maxillary prominences initially respond to signals from both regions, with GATA3 playing a crucial role in separating the upper and lower jaw domains during development by influencing BMP4 and FGF8 gene regulatory networks.
Article
Biochemistry & Molecular Biology
Charlotte Rat, Cedric Heindl, Hannes Neuweiler
Summary: Domain swap is a mechanism of protein dimerization in which two interacting domains exchange parts of their structure. Spidroin CTDs play a critical role in silk formation by inducing structural transitions, and the domain swap of spidroin CTDs results in an entropic penalty that prepares them for refolding during silk formation.
Article
Chemistry, Physical
Jiachen Li, Zehua Chen, Weitao Yang
Summary: This study introduces the G(RS)T(0) and G(RS)T(RS) methods, which combine the RS Green's function and T-matrix approximation to compute quasiparticle energies in molecular systems, comparing their performance with G(0)T(0) and G(0)W(0) methods for valence and core states, as well as the dependence of G(0)T(0) method on density functional approximations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Yuncai Mei, Zehua Chen, Weitao Yang
Summary: The developed second-order correction eliminates systematic delocalization error in commonly used density functional approximations. It provides highly accurate approximation of ground-state orbital energies for small and medium-size molecules, with excellent predictions for ionization potentials, electron affinities, photoemission spectrum, and photoexcitation energies. This correction shows great potential for broad applications in computational spectroscopy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Haoran Pang, Lindsey M. Walker, Alexey Silakov, Pan Zhang, Weitao Yang, Sean J. Elliott, Kenichi Yokoyama
Summary: The diversity of reactions catalyzed by radical S-adenosyl-L-methionine (SAM) enzymes is achieved in part through various mechanisms to quench radical intermediates. Among the SPASM-twitch family, MoaA serves as a representative member with unique cyclization of GTP involving an auxiliary 4Fe-4S cluster. The radical quenching step in MoaA involves a proton-coupled electron transfer mechanism, providing detailed insights into radical SAM enzyme catalysis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Shichen Lin, Daoling Peng, Weitao Yang, Feng Long Gu, Zhenggang Lan
Summary: The dissociation of hydrogen atoms from formaldehyde in the lowest triplet state was studied using a high-dimensional machine-learning potential energy surface model. The use of a deep-learning neural network to represent the PES function allowed for accurate simulations and exploration of vibrational excitation effects on the dissociation dynamics. The results showed that specific vibrational excitations enhance the probability of hydrogen atom dissociation in the T-1 state.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yuncai Mei, Jincheng Yu, Zehua Chen, Neil Qiang Su, Weitao Yang
Summary: In recent years, the Yang laboratory has developed a series of scaling correction (SC) methods to reduce and eliminate the delocalization error in density functional approximations (DFAs) within density functional theory (DFT). This work presents the development of LibSC, a reliable and efficient implementation for the global scaling correction (GSC) method and the localized orbital scaling correction (LOSC) method. LibSC serves as a lightweight and open-source library that can be easily accessed and integrated into quantum chemistry packages for calculations with SC methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Jiachen Li, Zehua Chen, Weitao Yang
Summary: This article introduces a method to calculate accurate energies using renormalized singles (RS) in multireference density functional theory (DFT). The method improves the original approach by using a modified RS Hamiltonian to calculate two-electron addition energies, providing accurate energy calculations for both ground and excited states.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Shu-Hao Yeh, Weitao Yang, Chao-Ping Hsu
Summary: The article introduces an improved method for thermally assisted-occupation density functional theory (TAO-DFT), namely rTAO and rTAO-1. These methods can simulate systems with strong static correlation in a simpler and more efficient way, and can capture accurate static correlation profiles.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Jiachen Li, Ye Jin, Neil Qiang Su, Weitao Yang
Summary: The localized orbital scaling correction (LOSC) applied in the Bethe-Salpeter equation (BSE) accurately predicts excitation energies for molecules, eliminating delocalization errors and approximating quasiparticle (QP) energies with accuracy comparable to or better than the GW Green's function approach, and at a much lower computational cost. The BSE/LOSC approach outperforms commonly used methods for predicting excitations with different characters, showing promise as an efficient method for calculating excitation energies in molecular systems.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Liang Peng, Daoling Peng, Feng Long Gu, Weitao Yang
Summary: Non-orthogonal localized molecular orbitals (NOL-MOs) are used in the divide-and-conquer (DC) linear scaling method, improving accuracy and transferability. A new regularized localization approach enhances smoothness of the NOLMOs. NOLMO-DC outperforms the original DC method in terms of accuracy for large conjugated systems and other systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Jiachen Li, Ye Jin, Patrick Rinke, Weitao Yang, Dorothea Golze
Summary: This paper presents a comprehensive benchmark study on various GW methodologies for molecular inner-shell excitations. Three GW schemes, including partial eigenvalue self consistency and a Hedin shift, show superior performance in computing absolute core-level energies. While all methods reproduce relative binding energies well, the eigenvalue self-consistent schemes and the Hedin shift yield the best results with mean absolute errors below 0.2 eV.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Weitao Yang, Jiachen Li, Dorothea Golze
Summary: In this study, the renormalized singles (RS) Green's function is applied in the Bethe-Salpeter equation (BSE)/GW approach to accurately predict neutral excitation energies of molecular systems. The BSE/GRSWRS method significantly outperforms other approaches in terms of accuracy and eliminates the dependence on the choice of density functional approximation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Dimitra Apostolidou, Pan Zhang, Weitao Yang, Piotr E. Marszalek
Summary: This study investigates the unfolding behavior and misfolding properties of the NanoLuc protein. The results show that introducing I91 domains can minimize the misfolding of Nluc in certain constructs. Additionally, simulations reveal the mechanical stability of Nluc and capture interesting unfolding intermediates.
Article
Materials Science, Multidisciplinary
Aaron Mahler, Jacob Williams, Neil Qiang Su, Weitao Yang
Summary: Density functional theory with commonly used approximations suffers from delocalization error, but the localized orbital scaling correction (LOSC) method can effectively correct this error by using localized orbitals. We extend the LOSC method to periodic systems and introduce a screened Coulomb kernel for energy correction. Experimental results show that the screened LOSC method consistently improves the band gap compared to the parent density functional approximation.
Article
Chemistry, Physical
Andrew M. Teale, Trygve Helgaker, Andreas Savin, Carlo Adamo, Balint Aradi, Alexei Arbuznikov, Paul W. Ayers, Evert Jan Baerends, Vincenzo Barone, Patrizia Calaminici, Eric Cances, Emily A. Carter, Pratim Kumar Chattaraj, Henry Chermette, Ilaria Ciofini, T. Daniel Crawford, Frank De Proft, John F. Dobson, Claudia Draxl, Thomas Frauenheim, Emmanuel Fromager, Patricio Fuentealba, Laura Gagliardi, Giulia Galli, Jiali Gao, Paul Geerlings, Nikitas Gidopoulos, Peter M. W. Gill, Paola Gori-Giorgi, Andreas Gorling, Tim Gould, Stefan Grimme, Oleg Gritsenko, Hans Jorgen Aagaard Jensen, Erin R. Johnson, Robert O. Jones, Martin Kaupp, Andreas M. Koster, Leeor Kronik, Anna Krylov, Simen Kvaal, Andre Laestadius, Mel Levy, Mathieu Lewin, Shubin Liu, Pierre-Francois Loos, Neepa T. Maitra, Frank Neese, John P. Perdew, Katarzyna Pernal, Pascal Pernot, Piotr Piecuch, Elisa Rebolini, Lucia Reining, Pina Romaniello, Adrienn Ruzsinszky, Dennis R. Salahub, Matthias Scheffler, Peter Schwerdtfeger, Viktor N. Staroverov, Jianwei Sun, Erik Tellgren, David J. Tozer, Samuel B. Trickey, Carsten A. Ullrich, Alberto Vela, Giovanni Vignale, Tomasz A. Wesolowski, Xin Xu, Weitao Yang
Summary: This paper provides an informal review and discussion on the history, present status, and future of density-functional theory (DFT) by 70 workers in the field. The format of a roundtable discussion allowed participants to express their views through 302 individual contributions to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper offers a comprehensive snapshot of DFT in 2022.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Jincheng Yu, Neil Qiang Su, Weitao Yang
Summary: This article emphasizes the importance of locality in physical space for understanding chemical reactivity. The concept of frontier molecular orbitalets (FMOLs) is introduced as a method for describing the reactivity of large systems. By locating the reactive region in chemical systems, FMOLs connect quantum mechanical treatments and chemical reactions. This approach provides insight into both energy and locality and has the potential for broad applications in the study of chemical reactions in large systems.