1
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Chakraborty A, Samant D, Sarkar R, Sangeet S, Prusty S, Roy S. RNA's Dynamic Conformational Selection and Entropic Allosteric Mechanism in Controlling Cascade Protein Binding Events. J Phys Chem Lett 2024; 15:6115-6125. [PMID: 38830201 DOI: 10.1021/acs.jpclett.4c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
In the TAR RNA of immunodeficiency viruses, an allosteric communication exists between a distant loop and a bulge. The bulge interacts with the TAT protein vital for transactivating viral RNA, while the loop interacts with cyclin-T1, contingent on TAT binding. Through extensive atomistic and free energy simulations, we investigate TAR-TAT binding in nonpathogenic bovine immunodeficiency virus (BIV) and pathogenic human immunodeficiency virus (HIV). Thermodynamic analysis reveals enthalpically driven binding in BIV and entropically favored binding in HIV. The broader global basin in HIV is attributed to binding-induced loop fluctuation, corroborated by nuclear magnetic resonance (NMR), indicating classical entropic allostery onset. While this loop fluctuation affects the TAT binding affinity, it generates a binding-competent conformation that aids subsequent effector (cyclin-T1) binding. This study underscores how two structurally similar apo-RNA scaffolds adopt distinct conformational selection mechanisms to drive enthalpic and entropic allostery, influencing protein affinity in the signaling cascade.
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Affiliation(s)
- Amrita Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Dibyamanjaree Samant
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Satyam Sangeet
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Sangram Prusty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
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2
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Huang R, Hua J, Ru M, Yu M, Wang L, Huang Y, Yan S, Zhang Q, Xu W. Superb Silk Hydrogels with High Adaptability, Bioactivity, and Versatility Enabled by Photo-Cross-Linking. ACS NANO 2024; 18:15312-15325. [PMID: 38809601 DOI: 10.1021/acsnano.4c05017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The exceptional biocompatibility and adaptability of hydrogels have garnered significant interest in the biomedical field for the fabrication of biomedical devices. However, conventional synthetic hydrogels still exhibit relatively weak and fragile properties. Drawing inspiration from the photosynthesis process, we developed a facile approach to achieve a harmonious combination of superior mechanical properties and efficient preparation of silk fibroin hydrogel through photo-cross-linking technology, accomplished within 60 s. The utilization of riboflavin and H2O2 enabled a sustainable cyclic photo-cross-linking reaction, facilitating the transformation from tyrosine to dityrosine and ultimately contributing to the formation of highly cross-linked hydrogels. These photo-cross-linking hydrogels exhibited excellent elasticity and restorability even after undergoing 1000 cycles of compression. Importantly, our findings presented that hydrogel-encapsulated adipose stem cells possess the ability to stimulate cell proliferation along with stem cell stemness. This was evidenced by the continuous high expression levels of OCT4 and SOX2 over 21 days. Additionally, the utilization of photo-cross-linking hydrogels can be extended to various material molding platforms, including microneedles, microcarriers, and bone screws. Consequently, this study offered a significant approach to fabricating biomedical hydrogels capable of facilitating real-time cell delivery, thereby introducing an innovative avenue for designing silk devices with exceptional machinability and adaptability in biomedical applications.
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Affiliation(s)
- Renyan Huang
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Jiahui Hua
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Min Ru
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Meng Yu
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Lu Wang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, School and Hospital of Stomatology, Shanxi Medical University, Taiyuan 030001, China
| | - Ying Huang
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Shuqin Yan
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Qiang Zhang
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
| | - Weilin Xu
- State Key Laboratory for Hubei New Textile Materials and Advanced Processing Technologies, School of Textile Science and Engineering, Wuhan Textile University, Wuhan 430200, China
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3
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Southern SA, Perras FA. Comparison of methods for the NMR measurement of motionally averaged dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107710. [PMID: 38901172 DOI: 10.1016/j.jmr.2024.107710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods' strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C-H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. We evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.
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Affiliation(s)
- Scott A Southern
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA
| | - Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA; Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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4
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Liu Z, Gillis TG, Raman S, Cui Q. A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery. eLife 2024; 12:RP92262. [PMID: 38836839 PMCID: PMC11152574 DOI: 10.7554/elife.92262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
New experimental findings continue to challenge our understanding of protein allostery. Recent deep mutational scanning study showed that allosteric hotspots in the tetracycline repressor (TetR) and its homologous transcriptional factors are broadly distributed rather than spanning well-defined structural pathways as often assumed. Moreover, hotspot mutation-induced allostery loss was rescued by distributed additional mutations in a degenerate fashion. Here, we develop a two-domain thermodynamic model for TetR, which readily rationalizes these intriguing observations. The model accurately captures the in vivo activities of various mutants with changes in physically transparent parameters, allowing the data-based quantification of mutational effects using statistical inference. Our analysis reveals the intrinsic connection of intra- and inter-domain properties for allosteric regulation and illustrate epistatic interactions that are consistent with structural features of the protein. The insights gained from this study into the nature of two-domain allostery are expected to have broader implications for other multi-domain allosteric proteins.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston UniversityBostonUnited States
| | - Thomas G Gillis
- Department of Biochemistry, University of WisconsinMadisonUnited States
| | - Srivatsan Raman
- Department of Biochemistry, University of WisconsinMadisonUnited States
- Department of Chemistry, University of WisconsinMadisonUnited States
- Department of Bacteriology, University of WisconsinMadisonUnited States
| | - Qiang Cui
- Department of Physics, Boston UniversityBostonUnited States
- Department of Chemistry, Boston UniversityBostonUnited States
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5
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Ray Chaudhuri N, Ghosh Dastidar S. Adaptive Workflows of Machine Learning Illuminate the Sequential Operation Mechanism of the TAK1's Allosteric Network. Biochemistry 2024; 63:1474-1492. [PMID: 38743619 DOI: 10.1021/acs.biochem.3c00643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Allostery is a fundamental mechanism driving biomolecular processes that holds significant therapeutic concern. Our study rigorously investigates how two distinct machine-learning algorithms uniquely classify two already close-to-active DFG-in states of TAK1, differing just by the presence or absence of its allosteric activator TAB1, from an ensemble mixture of conformations (obtained from 2.4 μs molecular dynamics (MD) simulations). The novelty, however, lies in understanding the deeper algorithmic potentials to systematically derive a diverse set of differential residue connectivity features that reconstruct the essential mechanistic architecture for TAK1-TAB1 allostery in such a close-to-active biochemical scenario. While the recursive, random forest-based workflow displays the potential of conducting discretized, hierarchical derivation of allosteric features, a multilayer perceptron-based approach gains considerable efficacy in revealing fluid connected patterns of features when hybridized with mutual information scoring. Interestingly, both pipelines benchmark similar directions of functional conformational changes for TAK1's activation. The findings significantly advance the depth of mechanistic understanding by highlighting crucial activation signatures along a directed C-lobe → activation loop → ATP pocket channel of information flow, including (1) the αF-αE biterminal alignments and (2) the "catalytic" drift of the activation loop toward kinase active site. Besides, some novel allosteric hotspots (K253, Y206, N189, etc.) are further recognized as TAB1 sensors, transducers, and responders, including a benchmark E70 mutation site, precisely mapping the important structural segments for sequential allosteric execution. Hence, our work demonstrates how to navigate through greater structural depths and dimensions of dynamic allosteric machineries just by leveraging standard ML methods in suitable streamlined workflows adaptive to the specific system and objectives.
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Affiliation(s)
- Nibedita Ray Chaudhuri
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India
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6
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Bernetti M, Bosio S, Bresciani V, Falchi F, Masetti M. Probing allosteric communication with combined molecular dynamics simulations and network analysis. Curr Opin Struct Biol 2024; 86:102820. [PMID: 38688074 DOI: 10.1016/j.sbi.2024.102820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Understanding the allosteric mechanisms within biomolecules involved in diseases is of paramount importance for drug discovery. Indeed, characterizing communication pathways and critical hotspots in signal transduction can guide a rational approach to leverage allosteric modulation for therapeutic purposes. While the atomistic signatures of allosteric processes are difficult to determine experimentally, computational methods can be a remarkable resource. Network analysis built on Molecular Dynamics simulation data is particularly suited in this respect and is gradually becoming of routine use. Herein, we collect the recent literature in the field, discussing different aspects and available options for network construction and analysis. We further highlight interesting refinements and extensions, eventually providing our perspective on this topic.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
| | - Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/Stefano__Bosio
| | - Veronica Bresciani
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/V_Bresciani
| | - Federico Falchi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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Coricello A, Nardone AJ, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Zhu W, Takagi Y, Richards NGJ. Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.16.541009. [PMID: 37292727 PMCID: PMC10245805 DOI: 10.1101/2023.05.16.541009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
How motions in enzymes might be linked to catalytic function is of considerable general interest. Recent advances in X-ray crystallography and cryogenic electron microscopy offer the promise of elucidating functionally relevant motions in proteins that are not easily amenable to study by other biophysical methods. Here we use 3D variability analysis (3DVA) on cryo-EM maps for wild type (WT) human asparagine synthetase (ASNS) and the R142I ASNS variant to identify conformational changes in the Arg-142 side chain, which mediates the formation of a catalytically relevant intramolecular tunnel. Our 3DVA results for WT ASNS are consistent with independent molecular dynamics (MD) simulations on a model generated from the X-ray structure of human ASNS. Moreover, MD simulations of computational models for the ASNS/β-aspartyl-AMP/MgPPi and R142I/β-aspartyl-AMP/MgPPi ternary complexes, suggest that the structural integrity of the tunnel is impaired in the R142I variant when β-aspartyl-AMP is present in the synthetase active site. The kinetic properties of the R142I ASNS variant support the proposed function of Arg-142. These studies illustrate the power of cryo-EM to identify localized motions and dissect the conformational landscape of large proteins. When combined with MD simulations, 3DVA is a powerful approach to understanding how conformational dynamics might regulate function in multi-domain enzymes possessing multiple active sites.
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Affiliation(s)
- Adriana Coricello
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - Alanya J Nardone
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, 09042 Cagliari, Italy
| | - Carmen Gratteri
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Matthijn Vos
- NanoImaging Core Facility, Centre de Resources et Recherches Technologiques, Institut Pasteur, 75015 Paris, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, 69367 Lyon, France
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Wen Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Yuichiro Takagi
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
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Tran QH, Eder OM, Winkler A. Dynamics-driven allosteric stimulation of diguanylate cyclase activity in a red light-regulated phytochrome. J Biol Chem 2024; 300:107217. [PMID: 38522512 PMCID: PMC11035067 DOI: 10.1016/j.jbc.2024.107217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Sensor-effector proteins integrate information from different stimuli and transform this into cellular responses. Some sensory domains, like red-light responsive bacteriophytochromes, show remarkable modularity regulating a variety of effectors. One effector domain is the GGDEF diguanylate cyclase catalyzing the formation of the bacterial second messenger cyclic-dimeric-guanosine monophosphate. While critical signal integration elements have been described for different phytochromes, a generalized understanding of signal processing and communication over large distances, roughly 100 Å in phytochrome diguanylate cyclases, is missing. Here we show that dynamics-driven allostery is key to understanding signal integration on a molecular level. We generated protein variants stabilized in their far-red-absorbing Pfr state and demonstrated by analysis of conformational dynamics using hydrogen-deuterium exchange coupled to mass spectrometry that single amino acid replacements are accompanied by altered dynamics of functional elements throughout the protein. We show that the conformational dynamics correlate with the enzymatic activity of these variants, explaining also the increased activity of a non-photochromic variant. In addition, we demonstrate the functional importance of mixed Pfr/intermediate state dimers using a fast-reverting variant that still enables wild-type-like fold-changes of enzymatic stimulation by red light. This supports the functional role of single protomer activation in phytochromes, a property that might correlate with the non-canonical mixed Pfr/intermediate-state spectra observed for many phytochrome systems. We anticipate our results to stimulate research in the direction of dynamics-driven allosteric regulation of different bacteriophytochrome-based sensor-effectors. This will eventually impact design strategies for the creation of novel sensor-effector systems for enriching the optogenetic toolbox.
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Affiliation(s)
- Quang Hieu Tran
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | | | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; BioTechMed Graz, Graz, Austria.
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9
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Erkip A, Erman B. Dynamically driven correlations in elastic net models reveal sequence of events and causality in proteins. Proteins 2024. [PMID: 38687146 DOI: 10.1002/prot.26697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/07/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
An explicit analytic solution is given for the Langevin equation applied to the Gaussian Network Model of a protein subjected to both a random and a deterministic periodic force. Synchronous and asynchronous components of time correlation functions are derived and an expression for phase differences in the time correlations of residue pairs is obtained. The synchronous component enables the determination of dynamic communities within the protein structure. The asynchronous component reveals causality, where the time correlation function between residues i and j differs depending on whether i is observed before j or vice versa, resulting in directional information flow. Driver and driven residues in the allosteric process of cyclophilin A and human NAD-dependent isocitrate dehydrogenase are determined by a perturbation-scanning technique. Factors affecting phase differences between fluctuations of residues, such as network topology, connectivity, and residue centrality, are identified. Within the constraints of the isotropic Gaussian Network Model, our results show that asynchronicity increases with viscosity and distance between residues, decreases with increasing connectivity, and decreases with increasing levels of eigenvector centrality.
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Affiliation(s)
- Albert Erkip
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Istanbul, Turkey
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Wang M, Xia S, Jiang C, He S, Xia J, Wang Z, Yuan X, Liu L, Chen J. Aggregation Inducing Reversible Conformational Isomerization of Surface Staple in Au 18SR 14 Nanoclusters. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311895. [PMID: 38660823 DOI: 10.1002/smll.202311895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/11/2024] [Indexed: 04/26/2024]
Abstract
The conformation of molecules and materials is crucial in determining their properties and applications. Here, this work explores the reversible transformation between two distinct conformational isomers in metal nanoclusters. This work demonstrates the successful manipulation of a controllable and reversible isomerization of Au18SR14 within an aqueous solution through two distinct methods: ethanol addition and pH adjustment. The initial driver is the alteration of the solution environment, leading to the aggregation of Au18SR14 protected by ligands with smaller steric hindrance. At the atomic level, the folding mode of the unique Au4SR5 staple underpins the observed structural transformation. The reversal of staple conformation leads to color shifting between green and orange-red, and tailors a second emission peak at 725 nm originating from charge transfer from the thiolate to the Au9 core. This work not only deepens the understanding of the surface structure and dual-emission of metal nanoparticles, but also enhances the comprehension of their isomerization.
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Affiliation(s)
- Meng Wang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao, 266071, P. R. China
| | - Shan Xia
- Department of Physics, School of Physical and Mathematical Sciences, Nanjing Tech University, 30 Puzhu South Road, Pukou District, Nanjing, Jiangsu, 210009, P. R. China
| | - Chengjia Jiang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao, 266071, P. R. China
| | - Shuyi He
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao, 266071, P. R. China
| | - Jianfei Xia
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao, 266071, P. R. China
- Qingdao Boting Hydrogen Age Ocean Technol R&D Ctr, Qingdao Boting Technol Co Ltd, Shandong Hydrogen Times Marine Technology Co Ltd, Qingdao, 266100, P. R. China
| | - Zonghua Wang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao, 266071, P. R. China
| | - Xun Yuan
- School of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Liren Liu
- Department of Physics, School of Physical and Mathematical Sciences, Nanjing Tech University, 30 Puzhu South Road, Pukou District, Nanjing, Jiangsu, 210009, P. R. China
| | - Jishi Chen
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao, 266071, P. R. China
- Qingdao Boting Hydrogen Age Ocean Technol R&D Ctr, Qingdao Boting Technol Co Ltd, Shandong Hydrogen Times Marine Technology Co Ltd, Qingdao, 266100, P. R. China
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11
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Lu H, Ye H, You L. Photoswitchable Cascades for Allosteric and Bidirectional Control over Covalent Bonds and Assemblies. J Am Chem Soc 2024. [PMID: 38620077 DOI: 10.1021/jacs.4c01240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Studies of complex systems and emerging properties to mimic biosystems are at the forefront of chemical research. Dynamic multistep cascades, especially those exhibiting allosteric regulation, are challenging. Herein, we demonstrate a versatile platform of photoswitchable covalent cascades toward remote and bidirectional control of reversible covalent bonds and ensuing assemblies. The relay of a photochromic switch, keto-enol equilibrium, and ring-chain equilibrium allows light-mediated reversible allosteric structural changes. The accompanying distinct reactivity further enables photoswitchable dynamic covalent bonding and release of substrates bidirectionally through alternating two wavelengths of light, essentially realizing light-mediated signaling cycles. The downfall of energy by covalent bond formation/scission upon photochemical reactions offers the driving force for the controlled direction of the cascade. To show the molecular diversity, photoswitchable on-demand assembly/disassembly of covalent polymers, including structurally reconfigurable polymers, was realized. This work achieves photoswitchable allosteric regulation of covalent architectures within dynamic multistep cascades, which has rarely been reported before. The results resemble allosteric control within biological signaling networks and should set the stage for many endeavors, such as dynamic assemblies, molecular motors, responsive polymers, and intelligent materials.
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Affiliation(s)
- Hanwei Lu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
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12
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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401150. [PMID: 38582512 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325011, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Haihong Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Ximiao Hou
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
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13
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Nerín-Fonz F, Cournia Z. Machine learning approaches in predicting allosteric sites. Curr Opin Struct Biol 2024; 85:102774. [PMID: 38354652 DOI: 10.1016/j.sbi.2024.102774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional sites. The advantages of allosteric modulators over orthosteric ones have sparked the development of numerous computational approaches, such as the identification of allosteric binding sites, to facilitate allosteric drug discovery. Building on the success of machine learning (ML) models for solving complex problems in biology and chemistry, several ML models for predicting allosteric sites have been developed. In this review, we provide an overview of these models and discuss future perspectives powered by the field of artificial intelligence such as protein language models.
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Affiliation(s)
- Francho Nerín-Fonz
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephesiou, Athens 11527, Greece; Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephesiou, Athens 11527, Greece; Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
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14
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Babbitt GA, Rajendran M, Lynch ML, Asare-Bediako R, Mouli LT, Ryan CJ, Srivastava H, Rynkiewicz P, Phadke K, Reed ML, Moore N, Ferran MC, Fokoue EP. ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison. Biophys J 2024:S0006-3495(24)00204-2. [PMID: 38515299 DOI: 10.1016/j.bpj.2024.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/16/2023] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale nonrandom machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted between homologous sites representative of different functional or mutational states can potentially identify local effects on binding interaction and protein evolution. In addition, comparisons of different (i.e., nonhomologous) sites within MD simulations could be employed to identify functional shifts in local time-coordinated dynamics indicative of logic gating within proteins. However, comparative MD analysis is challenged by the large fraction of protein motion caused by random thermal noise in the surrounding solvent. Therefore, properly denoised MD comparisons could reveal functional sites involving these machine-like dynamics with good accuracy. Here, we introduce ATOMDANCE, a user-interfaced suite of comparative machine learning-based denoising tools designed for identifying functional sites and the patterns of coordinated motion they can create within MD simulations. ATOMDANCE-maxDemon4.0 employs Gaussian kernel functions to compute site-wise maximum mean discrepancy between learned features of motion, thereby assessing denoised differences in the nonrandom motions between functional or evolutionary states (e.g., ligand bound versus unbound, wild-type versus mutant). ATOMDANCE-maxDemon4.0 also employs maximum mean discrepancy to analyze potential random amino acid replacements allowing for a site-wise test of neutral versus nonneutral evolution on the divergence of dynamic function in protein homologs. Finally, ATOMDANCE-Choreograph2.0 employs mixed-model analysis of variance and graph network to detect regions where time-synchronized shifts in dynamics occur. Here, we demonstrate ATOMDANCE's utility for identifying key sites involved in dynamic responses during functional binding interactions involving DNA, small-molecule drugs, and virus-host recognition, as well as understanding shifts in global and local site coordination occurring during allosteric activation of a pathogenic protease.
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Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York.
| | - Madhusudan Rajendran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Miranda L Lynch
- Hauptmann Woodward Medical Research Institute, Buffalo, New York
| | - Richmond Asare-Bediako
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Leora T Mouli
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Cameron J Ryan
- McQuaid Jesuit High School Computer Club, Rochester, New York
| | | | - Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Kavya Phadke
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Makayla L Reed
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Nadia Moore
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Maureen C Ferran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Ernest P Fokoue
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York.
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15
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Skeens E, Sinha S, Ahsan M, D’Ordine AM, Jogl G, Palermo G, Lisi GP. High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9. SCIENCE ADVANCES 2024; 10:eadl1045. [PMID: 38446895 PMCID: PMC10917355 DOI: 10.1126/sciadv.adl1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Souvik Sinha
- Department of Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Alexandra M. D’Ordine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA, USA
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
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16
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Bhat ZA, Khan MM, Rehman A, Iqbal J, Sanjeev BS, Madhumalar A. MD simulations indicate Omicron P132H of SARS-CoV-2 M pro is a potential allosteric mutant involved in modulating the dynamics of catalytic site entry loop. Int J Biol Macromol 2024; 262:130077. [PMID: 38346625 DOI: 10.1016/j.ijbiomac.2024.130077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
The SARS-CoV-2 main protease Mpro, essential for viral replication is an important drug target. It plays a critical role in processing viral polyproteins necessary for viral replication assembly. One of the predominant SARS-CoV-2 Mpro mutations of Omicron variant is Pro132His. Structurally, this mutation site is located ∼22 Å away from the catalytic site. The solved crystal structure of this mutant in complex with inhibitors as well as its reported catalytic efficiency did not show any difference with respect to the wild type. Thus, the mutation was concluded to be non-allosteric. Based on microsecond long MD simulation of the Pro132His mutant and wild type, we show that Pro132His mutation affects the conformational equilibrium with more population of conformational substates having open catalytic site, modulated by the dynamics of the catalytic site entry loop, implying the allosteric nature of this mutation. The structural analysis indicates that rearrangement of hydrogen bonds between His132 and adjacent residues enhances the dynamics of the linker, which in turn is augmented by the inherent dynamic flexibility of the catalytic pocket entry site due to the presence of charged residues. The altered dynamics leading to loss of secondary structures corroborate well with the reported compromised thermal stability.
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Affiliation(s)
- Zahoor Ahmad Bhat
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohd Muzammil Khan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Ayyub Rehman
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Jawed Iqbal
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - B S Sanjeev
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj -211012, India
| | - Arumugam Madhumalar
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India.
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17
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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18
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Liu Z, Gillis T, Raman S, Cui Q. A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.06.552196. [PMID: 37662419 PMCID: PMC10473640 DOI: 10.1101/2023.08.06.552196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
New experimental findings continue to challenge our understanding of protein allostery. Recent deep mutational scanning study showed that allosteric hotspots in the tetracycline repressor (TetR) and its homologous transcriptional factors are broadly distributed rather than spanning well-defined structural pathways as often assumed. Moreover, hotspot mutation-induced allostery loss was rescued by distributed additional mutations in a degenerate fashion. Here, we develop a two-domain thermodynamic model for TetR, which readily rationalizes these intriguing observations. The model accurately captures the in vivo activities of various mutants with changes in physically transparent parameters, allowing the data-based quantification of mutational effects using statistical inference. Our analysis reveals the intrinsic connection of intra- and inter-domain properties for allosteric regulation and illustrate epistatic interactions that are consistent with structural features of the protein. The insights gained from this study into the nature of two-domain allostery are expected to have broader implications for other multidomain allosteric proteins.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston University, Boston, United States
| | - Thomas Gillis
- Department of Biochemistry, University of Wisconsin, Madison, United States
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, United States
- Department of Chemistry, University of Wisconsin, Madison, United States
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Qiang Cui
- Department of Physics, Boston University, Boston, United States
- Department of Chemistry, Boston University, Boston, United States
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19
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García-Morales A, Pulido NO, Balleza D. Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:77-90. [PMID: 37777680 DOI: 10.1007/s00249-023-01682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/06/2023] [Accepted: 08/20/2023] [Indexed: 10/02/2023]
Abstract
How a protein propagates the conformational changes throughout its structure remains largely unknown. In thermosensitive TRP channels, this allosteric communication is triggered by ligand interaction or in response to temperature changes. Because dynamic allostery suggests a dynamic role of disordered regions, in this work we set out to thoroughly evaluate these regions in six thermosensitive TRP channels. Thus, by contrasting the intrinsic flexibility of the transmembrane region as a function of the degree of disorder in those proteins, we discovered several residues that do not show a direct correlation in both parameters. This kind of structural discrepancy revealed residues that are either reported to be dynamic, functionally relevant or are involved in signal propagation and probably part of allosteric networks. These discrepant, potentially dynamic regions are not exclusive of TRP channels, as this same correlation was found in the Kv Shaker channel.
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Affiliation(s)
- Abigail García-Morales
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Tecnológico Nacional de México, Calz. Miguel Angel de Quevedo 2779 Col Formando Hogar, 91897, Veracruz, Ver, Mexico
| | - Nancy O Pulido
- Escuela de Ingeniería y Ciencias, Instituto Tecnológico y de Estudios Superiores de Monterrey, Cuernavaca, Mexico
| | - Daniel Balleza
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Tecnológico Nacional de México, Calz. Miguel Angel de Quevedo 2779 Col Formando Hogar, 91897, Veracruz, Ver, Mexico.
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20
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Casadevall G, Casadevall J, Duran C, Osuna S. The shortest path method (SPM) webserver for computational enzyme design. Protein Eng Des Sel 2024; 37:gzae005. [PMID: 38431867 DOI: 10.1093/protein/gzae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | | | - Cristina Duran
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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21
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Sinha S, Molina Vargas A, Arantes P, Patel A, O’Connell M, Palermo G. Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a. Nucleic Acids Res 2024; 52:906-920. [PMID: 38033317 PMCID: PMC10810222 DOI: 10.1093/nar/gkad1127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. It utilizes a CRISPR RNA (crRNA) to target RNA sequences and trigger a composite active site formed by two 'Higher Eukaryotes and Prokaryotes Nucleotide' (HEPN) domains, cleaving any solvent-exposed RNA. In this system, an intriguing form of allosteric communication controls the RNA cleavage activity, yet its molecular details are unknown. Here, multiple-microsecond molecular dynamics simulations are combined with graph theory to decipher this intricate activation mechanism. We show that the binding of a target RNA acts as an allosteric effector, by amplifying the communication signals over the dynamical noise through interactions of the crRNA at the buried HEPN1-2 interface. By introducing a novel Signal-to-Noise Ratio (SNR) of communication efficiency, we reveal critical allosteric residues-R377, N378, and R973-that rearrange their interactions upon target RNA binding. Alanine mutation of these residues is shown to select target RNA over an extended complementary sequence beyond guide-target duplex for RNA cleavage, establishing the functional significance of these hotspots. Collectively our findings offer a fundamental understanding of the Cas13a mechanism of action and pave new avenues for the development of highly selective RNA-based cleavage and detection tools.
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Affiliation(s)
- Souvik Sinha
- Department of Bioengineering, University of California Riverside, Riverside, CA , 92521, USA
| | - Adrian M Molina Vargas
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, Riverside, CA , 92521, USA
| | - Amun Patel
- Department of Bioengineering, University of California Riverside, Riverside, CA , 92521, USA
| | - Mitchell R O’Connell
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA , 92521, USA
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
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22
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Kish M, Ivory DP, Phillips JJ. Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry. J Am Chem Soc 2024; 146:298-307. [PMID: 38158228 PMCID: PMC10786028 DOI: 10.1021/jacs.3c08934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need in molecular biology and drug discovery to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme glycogen phosphorylase is a clinical target of great interest to treat type II diabetes and metastatic cancers. Here, we developed a time-resolved nonequilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach capable of precisely locating dynamic structural changes during allosteric activation and inhibition of glycogen phosphorylase. We resolved obligate transient changes in the localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect with a common structurally dynamic motif. This mass spectrometry approach uniquely stands to discover local transient structural dynamics and could be used broadly to identify features that influence the structural transitions of proteins.
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Affiliation(s)
- Monika Kish
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Dylan P. Ivory
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Jonathan J. Phillips
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
- Alan
Turing Institute, British Library, London NW1 2DB, U.K.
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23
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Guo J, Liu H. The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics. Curr Med Chem 2024; 31:2839-2840. [PMID: 38904158 DOI: 10.2174/092986733120240405144035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Affiliation(s)
- Jingjing Guo
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
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24
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Khan T, Das N, Negi KS, Bhowmik S, Sen P. Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability. Int J Biol Macromol 2023; 253:127100. [PMID: 37778586 DOI: 10.1016/j.ijbiomac.2023.127100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.
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Affiliation(s)
- Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Suman Bhowmik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India.
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25
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Henriksen HC, Sowers AJ, Travis CR, Vulpis TD, Cope TA, Ouslander SK, Russell AF, Gagné MR, Pophristic V, Liu Z, Waters ML. Stimulus-Induced Relief of Intentionally Incorporated Frustration Drives Refolding of a Water-Soluble Biomimetic Foldamer. J Am Chem Soc 2023; 145:27672-27679. [PMID: 38054648 DOI: 10.1021/jacs.3c09883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Frustrated, or nonoptimal, interactions have been proposed to be essential to a protein's ability to display responsive behavior such as allostery, conformational signaling, and signal transduction. However, the intentional incorporation of frustrated noncovalent interactions has not been explored as a design element in the field of dynamic foldamers. Here, we report the design, synthesis, characterization, and molecular dynamics simulations of the first dynamic water-soluble foldamer that, in response to a stimulus, exploits relief of frustration in its noncovalent network to structurally rearrange from a pleated to an intercalated columnar structure. Thus, relief of frustration provides the energetic driving force for structural rearrangement. This work represents a previously unexplored design element for the development of stimulus-responsive systems that has potential application to materials chemistry, synthetic biology, and molecular machines.
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Affiliation(s)
- Hanne C Henriksen
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Adam J Sowers
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher R Travis
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Troy D Vulpis
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas A Cope
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sarah K Ouslander
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alexander F Russell
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michel R Gagné
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Vojislava Pophristic
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028-1701 , United States
| | - Zhiwei Liu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028-1701 , United States
| | - Marcey L Waters
- Department of Chemistry, CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
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26
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Romanuka J, Folkers GE, Gnida M, Kovačič L, Wienk H, Kaptein R, Boelens R. Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery. Proc Natl Acad Sci U S A 2023; 120:e2311240120. [PMID: 38019859 PMCID: PMC10710081 DOI: 10.1073/pnas.2311240120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.
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Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Manuel Gnida
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Lidija Kovačič
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Robert Kaptein
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
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27
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Bao Y, Xu Y, Jia F, Li M, Xu R, Zhang F, Guo J. Allosteric inhibition of myosin by phenamacril: a synergistic mechanism revealed by computational and experimental approaches. PEST MANAGEMENT SCIENCE 2023; 79:4977-4989. [PMID: 37540764 DOI: 10.1002/ps.7699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Myosin plays a crucial role in cellular processes, while its dysfunction can lead to organismal malfunction. Phenamacril (PHA), a highly species-specific and non-competitive inhibitor of myosin I (FgMyoI) from Fusarium graminearum, has been identified as an effective fungicide for controlling plant diseases caused by partial Fusarium pathogens, such as wheat scab and rice bakanae. However, the molecular basis of its action is still unclear. RESULTS This study used multiple computational approaches first to elucidate the allosteric inhibition mechanism of FgMyoI by PHA at the atomistic level. The results indicated the increase of adenosine triphosphate (ATP) binding affinity upon PHA binding, which might impede the release of hydrolysis products. Furthermore, simulations revealed a broadened outer cleft and a significantly more flexible interface for actin binding, accompanied by a decrease in signaling transduction from the catalytic center to the actin-binding interface. These various effects might work together to disrupt the actomyosin cycle and hinder the ability of motor to generate force. Our experimental results further confirmed that PHA reduces the enzymatic activity of myosin and its binding with actin. CONCLUSION Therefore, our findings demonstrated that PHA might suppress the function of myosin through a synergistic mechanism, providing new insights into myosin allostery and offering new avenues for drug/fungicide discovery targeting myosin. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fangying Jia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ran Xu
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jingjing Guo
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
- Engineering Research Centre of Applied Technology on Machine Translation and Artificial Intelligence, Macao Polytechnic University, Macao, China
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28
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Flagg MP, Lam B, Lam DK, Le TM, Kao A, Slaiwa YI, Hampton RY. Exploring the "misfolding problem" by systematic discovery and analysis of functional-but-degraded proteins. Mol Biol Cell 2023; 34:ar125. [PMID: 37729018 PMCID: PMC10848938 DOI: 10.1091/mbc.e23-06-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
In both health and disease, the ubiquitin-proteasome system (UPS) degrades point mutants that retain partial function but have decreased stability compared with their wild-type counterparts. This class of UPS substrate includes routine translational errors and numerous human disease alleles, such as the most common cause of cystic fibrosis, ΔF508-CFTR. Yet, there is no systematic way to discover novel examples of these "minimally misfolded" substrates. To address that shortcoming, we designed a genetic screen to isolate functional-but-degraded point mutants, and we used the screen to study soluble, monomeric proteins with known structures. These simple parent proteins yielded diverse substrates, allowing us to investigate the structural features, cytotoxicity, and small-molecule regulation of minimal misfolding. Our screen can support numerous lines of inquiry, and it provides broad access to a class of poorly understood but biomedically critical quality-control substrates.
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Affiliation(s)
- Matthew P. Flagg
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Breanna Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Darren K. Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Tiffany M. Le
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Andy Kao
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Yousif I. Slaiwa
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
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29
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Hofmann H. All over or overall - Do we understand allostery? Curr Opin Struct Biol 2023; 83:102724. [PMID: 37898005 DOI: 10.1016/j.sbi.2023.102724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/30/2023]
Abstract
Allostery is probably the most important concept in the regulation of cellular processes. Models to explain allostery are plenty. Each sheds light on different aspects but their entirety conveys an ambiguous feeling of comprehension and disappointment. Here, I discuss the most popular allostery models, their roots, similarities, and limitations. All of them are thermodynamic models. Naturally this bears a certain degree of redundancy, which forms the center of this review. After sixty years, many questions remain unanswered, mainly because our human longing for causality as base for understanding is not satisfied by thermodynamics alone. A description of allostery in terms of pathways, i.e., as a temporal chain of events, has been-, and still is-, a missing piece of the puzzle.
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Affiliation(s)
- Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100 Rehovot, Israel.
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30
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Wu GY, Zhu HM, Li H, Zhang K, Zhang X, Yan D, Zhang XD, Lin L, Lu Z. The impact of aggregation of AIE and ACQ moiety-integrating material on the excited state dynamics. RSC Adv 2023; 13:33911-33917. [PMID: 38020029 PMCID: PMC10658659 DOI: 10.1039/d3ra06359c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023] Open
Abstract
The investigation of the properties of aggregate materials is highly interesting because the process of aggregation can result in the disappearance of original properties and the emergence of new ones. Here, a novel fluorescent material (TPEIP), which synergistically combines aggregation-induced emission (AIE) and aggregation caused quenching (ACQ) moieties, was first synthesized by the cyclization reaction of 2,3-diamino-phenazine with 4-tetraphenylenthenealdehyde. We controlled the degree of aggregation of TPEIP to shed light on the impact of the aggregation on the excited state dynamics. TPEIP aggregation realized control over the Intersystem Crossing (ISC) rates and, in turn, the suppression of triplet excited states in MeOH, EtOH or via the simple addition of water to TPEIP solutions in DMSO. From global target analysis, the time scale was 966.2 ps for ISC for TPEIP in DMSO, but it was 860 ps in the case of TPEIP solutions featuring 5% water. The dynamics of TPEIP excited states undergo significant changes as the degree of aggregation increases. Notably, the lifetime of singlet excited states decreases, and there was a gradual diminishment in triplet states.
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Affiliation(s)
- Gui-Yuan Wu
- Anhui Province Key Laboratory of Optoelectronic Material Science and Technology, School of Physics and Electronic Information, Anhui Normal University Wuhu 241002 China
| | - Hui-Min Zhu
- Anhui Province Key Laboratory of Optoelectronic Material Science and Technology, School of Physics and Electronic Information, Anhui Normal University Wuhu 241002 China
| | - Hao Li
- Anhui Province Key Laboratory of Optoelectronic Material Science and Technology, School of Physics and Electronic Information, Anhui Normal University Wuhu 241002 China
| | - Kai Zhang
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University Jinan 250014 China
| | - Xianyi Zhang
- Anhui Province Key Laboratory of Optoelectronic Material Science and Technology, School of Physics and Electronic Information, Anhui Normal University Wuhu 241002 China
| | - Dong Yan
- Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University Wuhu 241002 China
| | - Xiu-Du Zhang
- Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University Wuhu 241002 China
| | - Lili Lin
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University Jinan 250014 China
| | - Zhou Lu
- Anhui Province Key Laboratory of Optoelectronic Material Science and Technology, School of Physics and Electronic Information, Anhui Normal University Wuhu 241002 China
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31
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Godbole SS, Dokholyan NV. Allosteric regulation of kinase activity in living cells. eLife 2023; 12:RP90574. [PMID: 37943025 PMCID: PMC10635643 DOI: 10.7554/elife.90574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities, making it difficult to specifically target one kinase, and allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss the methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or 'sensors,' are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.
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Affiliation(s)
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
- Department of Biomedical Engineering, Penn State University, University ParkHersheyUnited States
- Department of Engineering Science and Mechanics, Penn State University, University ParkHersheyUnited States
- Department of Biochemistry & Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Chemistry, Penn State University, University ParkHersheyUnited States
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32
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Guo Z, Wang L, Rao D, Liu W, Xue M, Fu Q, Lu M, Su L, Chen S, Wang B, Wu J. Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77. J Chem Inf Model 2023; 63:6118-6128. [PMID: 37768640 DOI: 10.1021/acs.jcim.3c00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Amylomaltases (AMs) play important roles in glycogen and maltose metabolism. However, the molecular mechanism is elusive. Here, we investigated the conformational dynamics of the 250s loop and catalytic mechanism of Thermus aquaticus TaAM using path-metadynamics and QM/MM MD simulations. The results demonstrate that the transition of the 250s loop from an open to closed conformation promotes polysaccharide sliding, leading to the ideal positioning of the acid/base. Furthermore, the conformational dynamics can also modulate the selectivity of hydrolysis and transglycosylation. The closed conformation of the 250s loop enables the tight packing of the active site for transglycosylation, reducing the energy penalty and efficiently preventing the penetration of water into the active site. Conversely, the partially closed conformation for hydrolysis results in a loosely packed active site, destabilizing the transition state. These computational findings guide mutation experiments and enable the identification of mutants with an improved disproportionation/hydrolysis ratio. The present mechanism is in line with experimental data, highlighting the critical role of conformational dynamics in regulating the catalytic reactivity of GHs.
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Affiliation(s)
- Zhiyong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Deming Rao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Miaomiao Xue
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Qisheng Fu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Mengwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
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33
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Godbole S, Dokholyan NV. Allosteric regulation of kinase activity in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549709. [PMID: 37503033 PMCID: PMC10370130 DOI: 10.1101/2023.07.19.549709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities making it difficult to specifically target one kinase, allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or "sensors" are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.
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Affiliation(s)
- Shivani Godbole
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Biomedical Engineering, Penn State University, University Park, PA 16802, USA
- Department of Engineering Science and Mechanics, Penn State University, University Park, PA 16802, USA
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
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34
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Robin AY, Brochier-Armanet C, Bertrand Q, Barette C, Girard E, Madern D. Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery. Mol Biol Evol 2023; 40:msad223. [PMID: 37797308 PMCID: PMC10583557 DOI: 10.1093/molbev/msad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023] Open
Abstract
Lactate dehydrogenase (LDH, EC.1.1.127) is an important enzyme engaged in the anaerobic metabolism of cells, catalyzing the conversion of pyruvate to lactate and NADH to NAD+. LDH is a relevant enzyme to investigate structure-function relationships. The present work provides the missing link in our understanding of the evolution of LDHs. This allows to explain (i) the various evolutionary origins of LDHs in eukaryotic cells and their further diversification and (ii) subtle phenotypic modifications with respect to their regulation capacity. We identified a group of cyanobacterial LDHs displaying eukaryotic-like LDH sequence features. The biochemical and structural characterization of Cyanobacterium aponinum LDH, taken as representative, unexpectedly revealed that it displays homotropic and heterotropic activation, typical of an allosteric enzyme, whereas it harbors a long N-terminal extension, a structural feature considered responsible for the lack of allosteric capacity in eukaryotic LDHs. Its crystallographic structure was solved in 2 different configurations typical of the R-active and T-inactive states encountered in allosteric LDHs. Structural comparisons coupled with our evolutionary analyses helped to identify 2 amino acid positions that could have had a major role in the attenuation and extinction of the allosteric activation in eukaryotic LDHs rather than the presence of the N-terminal extension. We tested this hypothesis by site-directed mutagenesis. The resulting C. aponinum LDH mutants displayed reduced allosteric capacity mimicking those encountered in plants and human LDHs. This study provides a new evolutionary scenario of LDHs that unifies descriptions of regulatory properties with structural and mutational patterns of these important enzymes.
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Affiliation(s)
- Adeline Y Robin
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, CNRS, UMR5558, Villeurbanne F-69622, France
| | - Quentin Bertrand
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Caroline Barette
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE, Grenoble 38000, France
| | - Eric Girard
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Dominique Madern
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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35
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Maria-Solano MA, Choi S. Dynamic allosteric networks drive adenosine A 1 receptor activation and G-protein coupling. eLife 2023; 12:RP90773. [PMID: 37656635 PMCID: PMC10473838 DOI: 10.7554/elife.90773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023] Open
Abstract
G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1 receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.
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Affiliation(s)
- Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
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36
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Skeens E, Sinha S, Ahsan M, D'Ordine AM, Jogl G, Palermo G, Lisi GP. High-Fidelity, Hyper-Accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554853. [PMID: 37662375 PMCID: PMC10473742 DOI: 10.1101/2023.08.25.554853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The Cas9-HF1, HypaCas9, and evoCas9 variants of the Cas9 endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in the Rec3 domain mediate specificity in these variants are poorly understood. Here, solution NMR and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and peculiar dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic HNH domain. The variants remodel the communication sourcing from the Rec3 α-helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.
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37
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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38
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Yu Y, O'Neill RT, Boulatov R, Widenhoefer RA, Craig SL. Allosteric control of olefin isomerization kinetics via remote metal binding and its mechanochemical analysis. Nat Commun 2023; 14:5074. [PMID: 37604905 PMCID: PMC10442431 DOI: 10.1038/s41467-023-40842-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
Allosteric control of reaction thermodynamics is well understood, but the mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here we report a molecular scaffold in which the rate of thermal E-to-Z isomerization of an alkene increases by a factor of as much as 104 in response to fast binding of a metal ion to a remote receptor site. A mechanochemical model of the olefin coupled to a compressive harmonic spring reproduces the observed acceleration quantitatively, adding the studied isomerization to the very few reactions demonstrated to be sensitive to extrinsic compressive force. The work validates experimentally the generalization of mechanochemical kinetics to compressive loads and demonstrates that the formalism of force-coupled reactivity offers a productive framework for the quantitative analysis of the molecular basis of allosteric control of reaction kinetics. Important differences in the effects of compressive vs. tensile force on the kinetic stabilities of molecules are discussed.
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Affiliation(s)
- Yichen Yu
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Robert T O'Neill
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Roman Boulatov
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK.
| | | | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, NC, 27708, USA.
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Corbella M, Pinto GP, Kamerlin SCL. Loop dynamics and the evolution of enzyme activity. Nat Rev Chem 2023; 7:536-547. [PMID: 37225920 DOI: 10.1038/s41570-023-00495-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/26/2023]
Abstract
In the early 2000s, Tawfik presented his 'New View' on enzyme evolution, highlighting the role of conformational plasticity in expanding the functional diversity of limited repertoires of sequences. This view is gaining increasing traction with increasing evidence of the importance of conformational dynamics in both natural and laboratory evolution of enzymes. The past years have seen several elegant examples of harnessing conformational (particularly loop) dynamics to successfully manipulate protein function. This Review revisits flexible loops as critical participants in regulating enzyme activity. We showcase several systems of particular interest: triosephosphate isomerase barrel proteins, protein tyrosine phosphatases and β-lactamases, while briefly discussing other systems in which loop dynamics are important for selectivity and turnover. We then discuss the implications for engineering, presenting examples of successful loop manipulation in either improving catalytic efficiency, or changing selectivity completely. Overall, it is becoming clearer that mimicking nature by manipulating the conformational dynamics of key protein loops is a powerful method of tailoring enzyme activity, without needing to target active-site residues.
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Affiliation(s)
- Marina Corbella
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Gaspar P Pinto
- Department of Chemistry, Uppsala University, Uppsala, Sweden
- Cortex Discovery GmbH, Regensburg, Germany
| | - Shina C L Kamerlin
- Department of Chemistry, Uppsala University, Uppsala, Sweden.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
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40
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Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. RNA-mediated Allosteric Activation in CRISPR-Cas13a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550797. [PMID: 37546822 PMCID: PMC10402131 DOI: 10.1101/2023.07.27.550797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. The protein uses a CRISPR RNA (crRNA) to target RNA sequences, which are cleaved by a composite active site formed by two 'Higher Eukaryotes and Prokaryotes Nucleotide' (HEPN) catalytic domains. In this system, an intriguing form of allosteric communication controls RNA cleavage activity, yet its molecular details are unknown. Here, multiple-microsecond molecular dynamics simulations are combined with graph theory and RNA cleavage assays to decipher this activation mechanism. We show that the binding of a target RNA acts as an allosteric effector of the spatially distant HEPN catalytic cleft, by amplifying the allosteric signals over the dynamical noise, that passes through the buried HEPN interface. Critical residues in this region - N378, R973, and R377 - rearrange their interactions upon target RNA binding, and alter allosteric signalling. Alanine mutation of these residues is experimentally shown to select target RNA over an extended complementary sequence beyond guide-target duplex, for RNA cleavage. Altogether, our findings offer a fundamental understanding of the Cas13a mechanism of action and pave new avenues for the development of more selective RNA-based cleavage and detection tools.
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41
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Alao JP, Obaseki I, Amankwah YS, Nguyen Q, Sugoor M, Unruh E, Popoola HO, Tehver R, Kravats AN. Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics. J Phys Chem B 2023; 127:5389-5409. [PMID: 37294929 PMCID: PMC10292203 DOI: 10.1021/acs.jpcb.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/17/2023] [Indexed: 06/11/2023]
Abstract
Grp94, an ER-localized molecular chaperone, is required for the folding and activation of many membrane and secretory proteins. Client activation by Grp94 is mediated by nucleotide and conformational changes. In this work, we aim to understand how microscopic changes from nucleotide hydrolysis can potentiate large-scale conformational changes of Grp94. We performed all-atom molecular dynamics simulations on the ATP-hydrolysis competent state of the Grp94 dimer in four different nucleotide bound states. We found that Grp94 was the most rigid when ATP was bound. ATP hydrolysis or nucleotide removal enhanced mobility of the N-terminal domain and ATP lid, resulting in suppression of interdomain communication. In an asymmetric conformation with one hydrolyzed nucleotide, we identified a more compact state, similar to experimental observations. We also identified a potential regulatory role of the flexible linker, as it formed electrostatic interactions with the Grp94 M-domain helix near the region where BiP is known to bind. These studies were complemented with normal-mode analysis of an elastic network model to investigate Grp94's large-scale conformational changes. SPM analysis identified residues that are important in signaling conformational change, many of which have known functional relevance in ATP coordination and catalysis, client binding, and BiP binding. Our findings suggest that ATP hydrolysis in Grp94 alters allosteric wiring and facilitates conformational changes.
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Affiliation(s)
- John Paul Alao
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ikponwmosa Obaseki
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yaa Sarfowah Amankwah
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Quinn Nguyen
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Meghana Sugoor
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Erin Unruh
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell,
Molecular, and Structural Biology Program, Department of Chemistry
& Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | | | - Riina Tehver
- Department
of Physics, Denison University, Granville, Ohio 43023, United States
| | - Andrea N. Kravats
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell,
Molecular, and Structural Biology Program, Department of Chemistry
& Biochemistry, Miami University, Oxford, Ohio 45056, United States
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42
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Konovalov KA, Wu CG, Qiu Y, Balakrishnan VK, Parihar PS, O’Connor MS, Xing Y, Huang X. Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A. J Chem Phys 2023; 158:215101. [PMID: 37260014 PMCID: PMC10238128 DOI: 10.1063/5.0150272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Mutations in protein phosphatase 2A (PP2A) are connected to intellectual disability and cancer. It has been hypothesized that these mutations might disrupt the autoinhibition and phosphorylation-induced activation of PP2A. Since they are located far from both the active and substrate binding sites, it is unclear how they exert their effect. We performed allosteric pathway analysis based on molecular dynamics simulations and combined it with biochemical experiments to investigate the autoinhibition of PP2A. In the wild type (WT), the C-arm of the regulatory subunit B56δ obstructs the active and substrate binding sites exerting a dual autoinhibition effect. We find that the disease mutant, E198K, severely weakens the allosteric pathways that stabilize the C-arm in the WT. Instead, the strongest allosteric pathways in E198K take a different route that promotes exposure of the substrate binding site. To facilitate the allosteric pathway analysis, we introduce a path clustering algorithm for lumping pathways into channels. We reveal remarkable similarities between the allosteric channels of E198K and those in phosphorylation-activated WT, suggesting that the autoinhibition can be alleviated through a conserved mechanism. In contrast, we find that another disease mutant, E200K, which is in spatial proximity of E198, does not repartition the allosteric pathways leading to the substrate binding site; however, it may still induce exposure of the active site. This finding agrees with our biochemical data, allowing us to predict the activity of PP2A with the phosphorylated B56δ and provide insight into how disease mutations in spatial proximity alter the enzymatic activity in surprisingly different mechanisms.
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Affiliation(s)
- Kirill A. Konovalov
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Yunrui Qiu
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Vijaya Kumar Balakrishnan
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Pankaj Singh Parihar
- McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Michael S. O’Connor
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yongna Xing
- Authors to whom correspondence should be addressed: and
| | - Xuhui Huang
- Authors to whom correspondence should be addressed: and
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43
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Zheng LE, Barethiya S, Nordquist E, Chen J. Machine Learning Generation of Dynamic Protein Conformational Ensembles. Molecules 2023; 28:4047. [PMID: 37241789 PMCID: PMC10220786 DOI: 10.3390/molecules28104047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Machine learning has achieved remarkable success across a broad range of scientific and engineering disciplines, particularly its use for predicting native protein structures from sequence information alone. However, biomolecules are inherently dynamic, and there is a pressing need for accurate predictions of dynamic structural ensembles across multiple functional levels. These problems range from the relatively well-defined task of predicting conformational dynamics around the native state of a protein, which traditional molecular dynamics (MD) simulations are particularly adept at handling, to generating large-scale conformational transitions connecting distinct functional states of structured proteins or numerous marginally stable states within the dynamic ensembles of intrinsically disordered proteins. Machine learning has been increasingly applied to learn low-dimensional representations of protein conformational spaces, which can then be used to drive additional MD sampling or directly generate novel conformations. These methods promise to greatly reduce the computational cost of generating dynamic protein ensembles, compared to traditional MD simulations. In this review, we examine recent progress in machine learning approaches towards generative modeling of dynamic protein ensembles and emphasize the crucial importance of integrating advances in machine learning, structural data, and physical principles to achieve these ambitious goals.
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Affiliation(s)
- Li-E Zheng
- Department of Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China;
| | - Shrishti Barethiya
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
| | - Erik Nordquist
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (S.B.); (E.N.)
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44
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Guo D, Hou Y, Liang H, Han L, Li B, Zhou B. Mechanism of Reduced Glutathione Induced Lysozyme Defolding and Molecular Self-Assembly. Foods 2023; 12:foods12101931. [PMID: 37238749 DOI: 10.3390/foods12101931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The distinctive assembly behaviors of lysozyme (Lys) feature prominently in food, materials, biomedicine, and other fields and have intrigued many scholars. Although our previous work suggested that reduced glutathione (GSH) could induce lysozyme to form interfacial films at the air/water interface, the underlying mechanism is still obscure. In the present study, the effects of GSH on the disulfide bond and protein conformation of lysozyme were investigated by fluorescence spectroscopy, circular dichroism spectroscopy, and infrared spectroscopy. The findings demonstrated that GSH was able to break the disulfide bond in lysozyme molecules through the sulfhydryl/disulfide bond exchange reaction, thereby unraveling the lysozyme. The β-sheet structure of lysozyme expanded significantly, while the contents of α-helix and β-turn decreased. Furthermore, the interfacial tension and morphology analysis supported that the unfolded lysozyme tended to arrange macroscopic interfacial films at the air/water interface. It was found that pH and GSH concentrations had an impact on the aforementioned processes, with higher pH or GSH levels having a positive effect. This paper on the exploration of the mechanism of GSH-induced lysozyme interface assembly and the development of lysozyme-based green coatings has better instructive significance.
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Affiliation(s)
- Dashan Guo
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
| | - Yuwei Hou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
| | - Hongshan Liang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingyu Han
- Key Lab of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
| | - Bin Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Zhou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China
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45
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Wang Y, Sensale S, Pedrozo M, Huang CM, Poirier MG, Arya G, Castro CE. Steric Communication between Dynamic Components on DNA Nanodevices. ACS NANO 2023; 17:8271-8280. [PMID: 37072126 PMCID: PMC10173695 DOI: 10.1021/acsnano.2c12455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among subcomponents. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce an approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion and the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sebastian Sensale
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Miguel Pedrozo
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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46
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Gordon BH, Liu P, Whittington AC, Silvers R, Miller BG. Biochemical methods to map and quantify allosteric motions in human glucokinase. Methods Enzymol 2023; 685:433-459. [PMID: 37245911 PMCID: PMC10308428 DOI: 10.1016/bs.mie.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Allosteric regulation of protein function is ubiquitous in biology. Allostery originates from ligand-mediated alterations in polypeptide structure and/or dynamics, which produce a cooperative kinetic or thermodynamic response to changing ligand concentrations. Establishing a mechanistic description of individual allosteric events requires both mapping the relevant changes in protein structure and quantifying the rates of differential conformational dynamics in the absence and presence of effectors. In this chapter, we describe three biochemical approaches to understand the dynamic and structural signatures of protein allostery using the well-established cooperative enzyme glucokinase as a case study. The combined application of pulsed proteolysis, biomolecular nuclear magnetic resonance spectroscopy and hydrogen-deuterium exchange mass spectrometry offers complementary information that can used to establish molecular models for allosteric proteins, especially when differential protein dynamics are involved.
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Affiliation(s)
- Blaine H Gordon
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Peilu Liu
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, United States
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Robert Silvers
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States.
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Tu G, Xu B, Luo D, Liu J, Liu Z, Chen G, Xue W. Multi-state Model-Based Identification of Cryptic Allosteric Sites on Human Serotonin Transporter. ACS Chem Neurosci 2023; 14:1686-1694. [PMID: 37067527 DOI: 10.1021/acschemneuro.3c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Serotonin transporter (SERT) plays a fundamental role in taking the synaptic cleft serotonin back to the presynaptic neuron. The discovery of allosteric SERT modulators represents the next-generation medication for psychiatric disorders such as depression. Here, based on the cryo-EM structures of ibogaine in complex with SERT in distinct conformations, the multiple functional structures of the transporter bound to serotonin, including outward-open (OOholo), outward-occluded (OCholo), and inward-open (IOholo and IOholo'), were carefully characterized by induced-fit docking Gaussian-accelerated molecular dynamics (IFD-GaMD) simulation and the free-energy landscape analysis. Further MM/GBSA binding free energy, per-residue contribution, and molecular interaction fingerprint calculations revealed the interaction variations of serotonin with SERT in functional structures, which confirmed the allostery of SERT during serotonin reuptake. Moreover, five unique cryptic allosteric sites, which are druggable and capable of targeting by small molecules, were identified on the characterized multistate structures. These results provide structural and energetic information for the molecular mechanism of serotonin reuptake and will provide opportunities for the development of novel therapeutics based on the identified new allosteric sites on SERT.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Binbin Xu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jin Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou 646000, China
| | - Gang Chen
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou 646000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Kish M, Subramanian S, Smith V, Lethbridge N, Cole L, Vollmer F, Bond NJ, Phillips JJ. Allosteric Regulation of Glycogen Phosphorylase by Order/Disorder Transition of the 250' and 280s Loops. Biochemistry 2023; 62:1360-1368. [PMID: 36989206 PMCID: PMC10116597 DOI: 10.1021/acs.biochem.2c00671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Allostery is a fundamental mechanism of protein activation, yet the precise dynamic changes that underlie functional regulation of allosteric enzymes, such as glycogen phosphorylase (GlyP), remain poorly understood. Despite being the first allosteric enzyme described, its structural regulation is still a challenging problem: the key regulatory loops of the GlyP active site (250' and 280s) are weakly stable and often missing density or have large b-factors in structural models. This led to the longstanding hypothesis that GlyP regulation is achieved through gating of the active site by (dis)order transitions, as first proposed by Barford and Johnson. However, testing this requires a quantitative measurement of weakly stable local structure which, to date, has been technically challenging in such a large protein. Hydrogen-deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for studying protein dynamics, and millisecond HDX-MS has the ability to measure site-localized stability differences in weakly stable structures, making it particularly valuable for investigating allosteric regulation in GlyP. Here, we used millisecond HDX-MS to measure the local structural perturbations of glycogen phosphorylase b (GlyPb), the phosphorylated active form (GlyPa), and the inhibited glucose-6 phosphate complex (GlyPb:G6P) at near-amino acid resolution. Our results support the Barford and Johnson hypothesis for GlyP regulation by providing insight into the dynamic changes of the key regulatory loops.
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Affiliation(s)
- Monika Kish
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
| | - Sivaraman Subramanian
- Living Systems Institute, Department of Physics, University of Exeter, Stocker Road, Exeter, EX4 6QD, U.K
| | | | | | - Lindsay Cole
- Applied Photophysics Ltd, Leatherhead, KT227BA, U.K
| | - Frank Vollmer
- Living Systems Institute, Department of Physics, University of Exeter, Stocker Road, Exeter, EX4 6QD, U.K
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Milstein Building, Granta Park, Cambridge, CB21 6GH, U.K
| | - Jonathan J Phillips
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
- Alan Turing Institute, British Library, London, NW1 2DB, U.K
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Anacleto J, Lento C, Sarpe V, Maqsood A, Mehrazma B, Schriemer D, Wilson DJ. Apparatus for Automated Continuous Hydrogen Deuterium Exchange Mass Spectrometry Measurements from Milliseconds to Hours. Anal Chem 2023; 95:4421-4428. [PMID: 36880265 PMCID: PMC9996604 DOI: 10.1021/acs.analchem.2c05003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique for protein characterization in industry and academia, complementing the "static" picture provided by classical structural biology with information about the dynamic structural changes that accompany biological function. Conventional hydrogen deuterium exchange experiments, carried out on commercially available systems, typically collect 4-5 exchange timepoints on a timescale ranging from tens of seconds to hours using a workflow that can require 24 h or more of continuous data collection for triplicate measurements. A small number of groups have developed setups for millisecond timescale HDX, allowing for the characterization of dynamic shifts in weakly structured or disordered regions of proteins. This capability is particularly important given the central role that weakly ordered protein regions often play in protein function and pathogenesis. In this work, we introduce a new continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) that allows automated, continuous or discrete labeling time measurements from milliseconds to hours. The device is composed almost entirely of "off-the-shelf" LC components and can acquire an essentially unlimited number of timepoints with substantially reduced runtimes compared to conventional systems.
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Affiliation(s)
- Joseph Anacleto
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Ayesha Maqsood
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Banafsheh Mehrazma
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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50
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Bassetto CAZ, Costa F, Guardiani C, Bezanilla F, Giacomello A. Noncanonical electromechanical coupling paths in cardiac hERG potassium channel. Nat Commun 2023; 14:1110. [PMID: 36849440 PMCID: PMC9971164 DOI: 10.1038/s41467-023-36730-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
Voltage-gated potassium channels are involved in many physiological processes such as nerve impulse transmission, the heartbeat, and muscle contraction. However, for many of them the molecular determinants of the gating mechanism remain elusive. Here, using a combination of theoretical and experimental approaches, we address this problem focusing on the cardiac hERG potassium channel. Network analysis of molecular dynamics trajectories reveals the presence of a kinematic chain of residues that couples the voltage sensor domain to the pore domain and involves the S4/S1 and S1/S5 subunit interfaces. Mutagenesis experiments confirm the role of these residues and interfaces in the activation and inactivation mechanisms. Our findings demonstrate the presence of an electromechanical transduction path crucial for the non-domain-swapped hERG channel gating that resembles the noncanonical path identified in domain-swapped K+ channels.
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Affiliation(s)
- Carlos A Z Bassetto
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Flavio Costa
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - Carlo Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Centro Interdisciplinario de Neurociencias, Facultad de Ciencias, Universidad de Valparaiso, Valparaiso, Chile.
| | - Alberto Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy.
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