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Xu T, Li Y, Gao X, Zhang L. Understanding the Fast-Triggering Unfolding Dynamics of FK-11 upon Photoexcitation of Azobenzene. J Phys Chem Lett 2024; 15:3531-3540. [PMID: 38526058 DOI: 10.1021/acs.jpclett.4c00091] [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: 03/26/2024]
Abstract
Photoswitchable molecules can control the activity and functions of biomolecules by triggering conformational changes. However, it is still challenging to fully understand such fast-triggering conformational evolution from nonequilibrium to equilibrium distribution at the molecular level. Herein, we successfully simulated the unfolding of the FK-11 peptide upon the photoinduced trans-to-cis isomerization of azobenzene based on the Markov state model. We found that the ensemble of FK-11 contains five conformational states, constituting two unfolding pathways. More intriguingly, we observed the microsecond-scale conformational propagation of the FK-11 peptide from the fully folded state to the equilibrium populations of the five states. The computed CD spectra match well with the experimental data, validating our simulation method. Overall, our study not only offers a protocol to study the photoisomerization-induced conformational changes of enzymes but also could orientate the rational design of a photoswitchable molecule to manipulate biological functions.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongfang Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fuzhou, Fujian 361005, China
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2
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Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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3
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Element- and enantiomer-selective visualization of molecular motion in real-time. Nat Commun 2023; 14:386. [PMID: 36693825 PMCID: PMC9873934 DOI: 10.1038/s41467-023-36047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023] Open
Abstract
Ultrafast optical-domain spectroscopies allow to monitor in real time the motion of nuclei in molecules. Achieving element-selectivity had to await the advent of time resolved X-ray spectroscopy, which is now commonly carried at X-ray free electron lasers. However, detecting light element that are commonly encountered in organic molecules, remained elusive due to the need to work under vacuum. Here, we present an impulsive stimulated Raman scattering (ISRS) pump/carbon K-edge absorption probe investigation, which allowed observation of the low-frequency vibrational modes involving specific selected carbon atoms in the Ibuprofen RS dimer. Remarkably, by controlling the probe light polarization we can preferentially access the enantiomer of the dimer to which the carbon atoms belong.
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4
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Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology. Biomolecules 2023; 13:biom13010124. [PMID: 36671509 PMCID: PMC9856150 DOI: 10.3390/biom13010124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Intense study of intrinsically disordered proteins (IDPs) did not begin in earnest until the late 1990s when a few groups, working independently, convinced the community that these 'weird' proteins could have important functions. Over the past two decades, it has become clear that IDPs play critical roles in a multitude of biological phenomena with prominent examples including coordination in signaling hubs, enabling gene regulation, and regulating ion channels, just to name a few. One contributing factor that delayed appreciation of IDP functional significance is the experimental difficulty in characterizing their dynamic conformations. The combined application of multiple methods, termed integrative structural biology, has emerged as an essential approach to understanding IDP phenomena. Here, we review some of the recent applications of the integrative structural biology philosophy to study IDPs.
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5
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Abstract
Major advances in X-ray sources including the development of circularly polarized and orbital angular momentum pulses make it possible to probe matter chirality at unprecedented energy regimes and with Ångström and femtosecond spatiotemporal resolutions. We survey the theory of stationary and time-resolved nonlinear chiral measurements that can be carried out in the X-ray regime using tabletop X-ray sources or large scale (XFEL, synchrotron) facilities. A variety of possible signals and their information content are discussed.
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Affiliation(s)
- Jérémy R Rouxel
- Université de Lyon, UJM-Saint-Etienne, CNRS, IOGS, Laboratoire Hubert Curien UMR 5516, Saint-Etienne F-42023, France
| | - Shaul Mukamel
- Department of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697-2025, United States
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6
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Kwan TOC, Kolek SA, Danson AE, Reis RI, Camacho IS, Shaw Stewart PD, Moraes I. Measuring Protein Aggregation and Stability Using High-Throughput Biophysical Approaches. Front Mol Biosci 2022; 9:890862. [PMID: 35651816 PMCID: PMC9149252 DOI: 10.3389/fmolb.2022.890862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Structure-function relationships of biological macromolecules, in particular proteins, provide crucial insights for fundamental biochemistry, medical research and early drug discovery. However, production of recombinant proteins, either for structure determination, functional studies, or to be used as biopharmaceutical products, is often hampered by their instability and propensity to aggregate in solution in vitro. Protein samples of poor quality are often associated with reduced reproducibility as well as high research and production expenses. Several biophysical methods are available for measuring protein aggregation and stability. Yet, discovering and developing means to improve protein behaviour and structure-function integrity remains a demanding task. Here, we discuss workflows that are made possible by adapting established biophysical methods to high-throughput screening approaches. Rapid identification and optimisation of conditions that promote protein stability and reduce aggregation will support researchers and industry to maximise sample quality, stability and reproducibility, thereby reducing research and development time and costs.
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Affiliation(s)
| | | | - Amy E. Danson
- National Physical Laboratory, Teddington, United Kingdom
| | - Rosana I. Reis
- National Physical Laboratory, Teddington, United Kingdom
| | | | - Patrick D. Shaw Stewart
- Douglas Instruments Ltd., Hungerford, United Kingdom
- *Correspondence: Patrick D. Shaw Stewart, ; Isabel Moraes,
| | - Isabel Moraes
- National Physical Laboratory, Teddington, United Kingdom
- *Correspondence: Patrick D. Shaw Stewart, ; Isabel Moraes,
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Sharma A, Khamar D, Cullen S, Hayden A, Hughes H. Innovative Drying Technologies for Biopharmaceuticals. Int J Pharm 2021; 609:121115. [PMID: 34547393 DOI: 10.1016/j.ijpharm.2021.121115] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 01/30/2023]
Abstract
In the past two decades, biopharmaceuticals have been a breakthrough in improving the quality of lives of patients with various cancers, autoimmune, genetic disorders etc. With the growing demand of biopharmaceuticals, the need for reducing manufacturing costs is essential without compromising on the safety, quality, and efficacy of products. Batch Freeze-drying is the primary commercial means of manufacturing solid biopharmaceuticals. However, Freeze-drying is an economically unfriendly means of production with long production cycles, high energy consumption and heavy capital investment, resulting in high overall costs. This review compiles some potential, innovative drying technologies that have not gained popularity for manufacturing parenteral biopharmaceuticals. Some of these technologies such as Spin-freeze-drying, Spray-drying, Lynfinity® Technology etc. offer a paradigm shift towards continuous manufacturing, whereas PRINT® Technology and MicroglassificationTM allow controlled dry particle characteristics. Also, some of these drying technologies can be easily scaled-up with reduced requirement for different validation processes. The inclusion of Process Analytical Technology (PAT) and offline characterization techniques in tandem can provide additional information on the Critical Process Parameters (CPPs) and Critical Quality Attributes (CQAs) during biopharmaceutical processing. These processing technologies can be envisaged to increase the manufacturing capacity for biopharmaceutical products at reduced costs.
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Affiliation(s)
- Ashutosh Sharma
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland.
| | - Dikshitkumar Khamar
- Sanofi, Manufacturing Science, Analytics and Technology (MSAT), IDA Industrial Park, Waterford X91TP27, Ireland
| | - Sean Cullen
- Gilead Sciences, Commercial Manufacturing, IDA Business & Technology Park, Carrigtwohill, Co. Cork T45DP77, Ireland
| | - Ambrose Hayden
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
| | - Helen Hughes
- Pharmaceutical and Molecular Biotechnology Research Centre (PMBRC), Waterford Institute of Technology, Main Campus, Cork Road, Waterford X91K0EK, Ireland
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8
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Hache F, Changenet P. Multiscale conformational dynamics probed by time-resolved circular dichroism from seconds to picoseconds. Chirality 2021; 33:747-757. [PMID: 34523161 DOI: 10.1002/chir.23359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 01/08/2023]
Abstract
Time-resolved circular dichroism has been developed for a few decades to investigate rapid conformational changes in (bio)molecules. In our group, we have come up with several experimental set-ups allowing us to study pico-nanosecond local phenomena in molecular systems as well as much slower effects occurring in proteins and DNA in the folding processes. After an overview of the worldwide realizations in this domain, we present emblematic experiments that we have carried out, spanning time domain from picoseconds to seconds.
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Affiliation(s)
- François Hache
- Optics and Biosciences Laboratory, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Pascale Changenet
- Optics and Biosciences Laboratory, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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9
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Théron L, Bonifacie A, Delabre J, Sayd T, Aubry L, Gatellier P, Ravel C, Chambon C, Astruc T, Rouel J, Santé-Lhoutellier V, Réfrégiers M, Wien F. Investigation by Synchrotron Radiation Circular Dichroism of the Secondary Structure Evolution of Pepsin under Oxidative Environment. Foods 2021; 10:foods10050998. [PMID: 34063224 PMCID: PMC8147470 DOI: 10.3390/foods10050998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Food processing affects the structure and chemical state of proteins. In particular, protein oxidation occurs and may impair protein properties. These chemical reactions initiated during processing can develop during digestion. Indeed, the physicochemical conditions of the stomach (oxygen pressure, low pH) favor oxidation. In that respect, digestive proteases may be affected as well. Yet, very little is known about the link between endogenous oxidation of digestive enzymes, their potential denaturation, and, therefore, food protein digestibility. Thus, the objective of this study is to understand how oxidative chemical processes will impact the pepsin secondary structure and its hydrolytic activity. The folding and unfolding kinetics of pepsin under oxidative conditions was determined using Synchrotron Radiation Circular Dichroism. SRCD gave us the possibility to monitor the rapid kinetics of protein folding and unfolding in real-time, giving highly resolved spectral data. The proteolytic activity of control and oxidized pepsin was investigated by MALDI-TOF mass spectrometry on a meat protein model, the creatine kinase. MALDI-TOF MS allowed a rapid evaluation of the proteolytic activity through peptide fingerprint. This study opens up new perspectives by shifting the digestion paradigm taking into account the gastric digestive enzyme and its substrate.
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Affiliation(s)
- Laetitia Théron
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
- Correspondence:
| | - Aline Bonifacie
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Jérémy Delabre
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), Plateforme D’exploration du Métabolisme Composante Protéomique (PFEMcp), F-63122 Saint Genès-Champanelle, France; (J.D.); (C.C.)
| | - Thierry Sayd
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Laurent Aubry
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Philippe Gatellier
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Christine Ravel
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Christophe Chambon
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), Plateforme D’exploration du Métabolisme Composante Protéomique (PFEMcp), F-63122 Saint Genès-Champanelle, France; (J.D.); (C.C.)
| | - Thierry Astruc
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Jacques Rouel
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Véronique Santé-Lhoutellier
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), UR370 Qualité des Produits Animaux, F-63122 Saint Genès-Champanelle, France; (A.B.); (T.S.); (L.A.); (P.G.); (C.R.); (T.A.); (J.R.); (V.S.-L.)
| | - Matthieu Réfrégiers
- DISCO Beamline, Synchrotron SOLEIL, F-91192 Gif-sur-Yvette, France; (M.R.); (F.W.)
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, F-45071 Orléans, France
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, F-91192 Gif-sur-Yvette, France; (M.R.); (F.W.)
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10
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Abstract
We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.
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Affiliation(s)
- Francois Auvray
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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