1
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Asil SM, Narayan M. Molecular interactions between gelatin-derived carbon quantum dots and Apo-myoglobin: Implications for carbon nanomaterial frameworks. Int J Biol Macromol 2024; 264:130416. [PMID: 38428776 DOI: 10.1016/j.ijbiomac.2024.130416] [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: 08/01/2023] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Carbon nanomaterials (CNMs), including carbon quantum dots (CQDs), have found widespread use in biomedical research due to their low toxicity, chemical tunability, and tailored applications. Yet, there exists a gap in our understanding of the molecular interactions between biomacromolecules and these novel carbon-centered platforms. Using gelatin-derived CQDs as a model CNM, we have examined the impact of this exemplar nanomaterial on apo-myoglobin (apo-Mb), an oxygen-storage protein. Intrinsic fluorescence measurements revealed that the CQDs induced conformational changes in the tertiary structure of native, partially unfolded, and unfolded states of apo-Mb. Titration with CQDs also resulted in significant changes in the secondary structural elements in both native (holo) and apo-Mb, as evidenced by the circular dichroism (CD) analyses. These changes suggested a transition from isolated helices to coiled-coils during the loss of the helical structure of the apo-protein. Infra-red spectroscopic data further underscored the interactions between the CQDs and the amide backbone of apo-myoglobin. Importantly, the CQDs-driven structural perturbations resulted in compromised heme binding to apo-myoglobin and, therefore, potentially can attenuate oxygen storage and diffusion. However, a cytotoxicity assay demonstrated the continued viability of neuroblastoma cells exposed to these carbon nanomaterials. These results, for the first time, provide a molecular roadmap of the interplay between carbon-based nanomaterial frameworks and biomacromolecules.
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Affiliation(s)
- Shima Masoudi Asil
- The Environmental Science & Engineering Program, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Mahesh Narayan
- The Department of Chemistry & Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA.
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2
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Michaelis M, Cupellini L, Mensch C, Perry CC, Delle Piane M, Colombi Ciacchi L. Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints. Chem Sci 2023; 14:8483-8496. [PMID: 37592980 PMCID: PMC10430726 DOI: 10.1039/d3sc02202a] [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: 05/01/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa Via G. Moruzzi 13 Pisa I-56124 Italy
| | - Carl Mensch
- Molecular Spectroscopy Research Group, Department of Chemistry, University of Antwerp Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 Torino 10129 Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
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3
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Lazzeri G, Micheletti C, Pasquali S, Faccioli P. RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias. Biophys J 2023; 122:3089-3098. [PMID: 37355771 PMCID: PMC10432211 DOI: 10.1016/j.bpj.2023.06.012] [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: 02/07/2023] [Revised: 05/03/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023] Open
Abstract
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. As a step forward in tackling these issues, we extend to RNA an enhanced path-sampling method previously successfully applied to proteins. In this scheme, the information about the RNA's native structure is harnessed by a soft history-dependent biasing force promoting the generation of productive folding trajectories in an all-atom force field with explicit solvent. A rigorous variational principle is then applied to minimize the effect of the bias. Here, we report on an application of this method to RNA molecules from 20 to 47 nucleotides long and increasing topological complexity. By comparison with analog simulations performed on small proteins with similar size and architecture, we show that the RNA folding landscape is significantly more frustrated, even for relatively small chains with a simple topology. The predicted RNA folding mechanisms are found to be consistent with the available experiments and some of the existing coarse-grained models. Due to its computational performance, this scheme provides a promising platform to efficiently gather atomistic RNA folding trajectories, thus retain the information about the chemical composition of the sequence.
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Affiliation(s)
- Gianmarco Lazzeri
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany; Physics Department of Trento University, Povo (Trento), Italy
| | | | - Samuela Pasquali
- Laboratoire Cibles Thérapeutiques et Conception de Médicaments, Université Paris Cité, Paris, France; Laboratoire Biologie Fonctionnelle et Adaptative, Université Paris Cité, Paris, France.
| | - Pietro Faccioli
- Physics Department of Trento University, Povo (Trento), Italy; INFN-TIFPA, Povo (Trento), Italy.
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4
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Study on the Interaction Mechanism of Methoxy Polyethylene Glycol Maleimide with Sweet Potato β-Amylase. Molecules 2023; 28:molecules28052188. [PMID: 36903434 PMCID: PMC10005407 DOI: 10.3390/molecules28052188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
In this study, sweet potato β-amylase (SPA) was modified by methoxy polyethylene glycol maleimide (molecular weight 5000, Mal-mPEG5000) to obtain the Mal-mPEG5000-SPA modified β-amylase and the interaction mechanism between SPA and Mal-mPEG5000 was investigated. the changes in the functional groups of different amide bands and modifications in the secondary structure of enzyme protein were analyzed using infrared spectroscopy and circular dichroism spectroscopy. The addition of Mal-mPEG5000 transformed the random curl in the SPA secondary structure into a helix structure, forming a folded structure. The Mal-mPEG5000 improved the thermal stability of SPA and protected the structure of the protein from breaking by the surrounding. The thermodynamic analysis further implied that the intermolecular forces between SPA and Mal-mPEG5000 were hydrophobic interactions and hydrogen bonds due to the positive values of ΔHθ and ΔSθ. Furthermore, the calorie titration data showed that the binding stoichiometry for the complexation of Mal-mPEG5000 to SPA was 1.26, and the binding constant was 1.256 × 107 mol/L. The binding reaction resulted from negative enthalpy, indicating that the interaction of SPA and Mal-mPEG5000 was induced by the van der Waals force and hydrogen bonding. The UV results showed the formation of non-luminescent material during the interaction, the Fluorescence results confirmed that the mechanism between SPA and Mal-mPEG5000 was static quenching. According to the fluorescence quenching measurement, the binding constant (KA) values were 4.65 × 104 L·mol-1 (298K), 5.56 × 104 L·mol-1 (308K), and 6.91 × 104 L·mol-1 (318K), respectively.
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5
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Sun H, Yao C, You K, Chen C, Liu S, Xu Z. Nanopore single-molecule biosensor in protein denaturation analysis. Anal Chim Acta 2023; 1243:340830. [PMID: 36697181 DOI: 10.1016/j.aca.2023.340830] [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: 11/10/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China.
| | - Chuan Yao
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Kaibo You
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Can Chen
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Shuoshuo Liu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Zhihong Xu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
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6
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Biasini E, Faccioli P. Functional, pathogenic, and pharmacological roles of protein folding intermediates. Proteins 2023. [PMID: 36779817 DOI: 10.1002/prot.26479] [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: 01/24/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Protein expression and function in eukaryotic cells are tightly harmonized processes modulated by the combination of different layers of regulation, including transcription, processing, stability, and translation of messenger RNA, as well as assembly, maturation, sorting, recycling, and degradation of polypeptides. Integrating all these pathways and the protein quality control machinery, deputed to avoid the production and accumulation of aberrantly folded proteins, determines protein homeostasis. Over the last decade, the combined development of accurate time-resolved experimental techniques and efficient computer simulations has opened the possibility of investigating biological mechanisms at atomic resolution with physics-based models. A meaningful example is the reconstruction of protein folding pathways at atomic resolution, which has enabled the characterization of the folding kinetics of biologically relevant globular proteins consisting of a few hundred amino acids. Combining these innovative computational technologies with rigorous experimental approaches reveals the existence of non-native metastable states transiently appearing along the folding process of such proteins. Here, we review the primary evidence indicating that these protein folding intermediates could play roles in disparate biological processes, from the posttranslational regulation of protein expression to disease-relevant protein misfolding mechanisms. Finally, we discuss how the information encoded into protein folding pathways could be exploited to design an entirely new generation of pharmacological agents capable of promoting the selective degradation of protein targets.
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Affiliation(s)
- Emiliano Biasini
- Department of Cellular Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Pietro Faccioli
- Department of Physics, University of Trento, Trento, Italy
- Trento Institute for Fundamental Physics and Applications, Italian Institute for Nuclear Physics, Trento, Italy
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7
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Liu Y, Liu CP, Mang CY, Wu KC. Upon DFT-D3 dispersion correction and ECD spectral confirmation, only several conformers can stably coexist for three fungal cycloaspeptides (A, D, G). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121710. [PMID: 35952587 DOI: 10.1016/j.saa.2022.121710] [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: 04/13/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Dispersion correction in theoretical determination of cyclopeptide conformations is emphasized. Whether in gas approximation or in solvation simulation, the density functional theory with London dispersion correction (DFT-D3) demonstrates that only 2-3 conformers can stably coexist for cycloaspeptides (A, D, G) at B3LYP-D3 and CAM-B3LYP-D3. Conformational rationality is confirmed by electronic circular dichroism (ECD). Whether for Cotton effect or for excitation energy, TD-B3LYP-D3 has better performances than TD-CAM-B3LYP-D3 because the former can better reproduce the experiment. A molecular orbital analysis is used to interpret ECD, where two energy bands observed in experiment originates from the ππ* transitions other than the σπ* transitions. Long-range correction and solvent effect make H-bonds shorten, and dispersion correction makes them further shorten.
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Affiliation(s)
- Yong Liu
- College of Pharmacy, Dali University, Dali 671000, China
| | - Cai-Ping Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Chao-Yong Mang
- College of Pharmacy, Dali University, Dali 671000, China.
| | - Ke-Chen Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
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8
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Long-range allostery mediates the regulation of plasminogen activator inhibitor-1 by cell adhesion factor vitronectin. J Biol Chem 2022; 298:102652. [PMID: 36444882 PMCID: PMC9731859 DOI: 10.1016/j.jbc.2022.102652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022] Open
Abstract
The serpin plasminogen activator inhibitor 1 (PAI-1) spontaneously undergoes a massive structural change from a metastable and active conformation, with a solvent-accessible reactive center loop (RCL), to a stable, inactive, or latent conformation, with the RCL inserted into the central β-sheet. Physiologically, conversion to the latent state is regulated by the binding of vitronectin, which hinders the latency transition rate approximately twofold. The molecular mechanisms leading to this rate change are unclear. Here, we investigated the effects of vitronectin on the PAI-1 latency transition using all-atom path sampling simulations in explicit solvent. In simulated latency transitions of free PAI-1, the RCL is quite mobile as is the gate, the region that impedes RCL access to the central β-sheet. This mobility allows the formation of a transient salt bridge that facilitates the transition; this finding rationalizes existing mutagenesis results. Vitronectin binding reduces RCL and gate mobility by allosterically rigidifying structural elements over 40 Å away from the binding site, thus blocking transition to the latent conformation. The effects of vitronectin are propagated by a network of dynamically correlated residues including a number of conserved sites that were previously identified as important for PAI-1 stability. Simulations also revealed a transient pocket populated only in the vitronectin-bound state, corresponding to a cryptic drug-binding site identified by crystallography. Overall, these results shed new light on PAI-1 latency transition regulation by vitronectin and illustrate the potential of path sampling simulations for understanding functional protein conformational changes and for facilitating drug discovery.
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9
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Zhao L, Zhang J, Zhang Y, Ye S, Zhang G, Chen X, Jiang B, Jiang J. Accurate Machine Learning Prediction of Protein Circular Dichroism Spectra with Embedded Density Descriptors. JACS AU 2021; 1:2377-2384. [PMID: 34977905 PMCID: PMC8715543 DOI: 10.1021/jacsau.1c00449] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 05/08/2023]
Abstract
A data-driven approach to simulate circular dichroism (CD) spectra is appealing for fast protein secondary structure determination, yet the challenge of predicting electric and magnetic transition dipole moments poses a substantial barrier for the goal. To address this problem, we designed a new machine learning (ML) protocol in which ordinary pure geometry-based descriptors are replaced with alternative embedded density descriptors and electric and magnetic transition dipole moments are successfully predicted with an accuracy comparable to first-principle calculation. The ML model is able to not only simulate protein CD spectra nearly 4 orders of magnitude faster than conventional first-principle simulation but also obtain CD spectra in good agreement with experiments. Finally, we predicted a series of CD spectra of the Trp-cage protein associated with continuous changes of protein configuration along its folding path, showing the potential of our ML model for supporting real-time CD spectroscopy study of protein dynamics.
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Affiliation(s)
- Luyuan Zhao
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jinxiao Zhang
- Guangxi
Key Laboratory of Electrochemical and Magneto-chemical Functional
Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541006, P. R. China
| | - Yaolong Zhang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Sheng Ye
- School
of Artificial Intelligence, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Guozhen Zhang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xin Chen
- Gusu
Laboratory of Materials, Suzhou, Jiangsu 215123, P. R. China
| | - Bin Jiang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jun Jiang
- Hefei
National Laboratory for Physical Sciences at the Microscale, Collaborative
Innovation Center of Chemistry for Energy Materials, School of Chemistry
and Materials Science, University of Science
and Technology of China, Hefei, Anhui 230026, P. R. China
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10
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Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. JACS AU 2021; 1:1217-1230. [PMID: 34467360 PMCID: PMC8397351 DOI: 10.1021/jacsau.1c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 05/12/2023]
Abstract
The pore-forming toxin cytolysin A (ClyA) is expressed as a large α-helical monomer that, upon interaction with membranes, undergoes a major conformational rearrangement into the protomer conformation, which then assembles into a cytolytic pore. Here, we investigate the folding kinetics of the ClyA monomer with single-molecule Förster resonance energy transfer spectroscopy in combination with microfluidic mixing, stopped-flow circular dichroism experiments, and molecular simulations. The complex folding process occurs over a broad range of time scales, from hundreds of nanoseconds to minutes. The very slow formation of the native state occurs from a rapidly formed and highly collapsed intermediate with large helical content and nonnative topology. Molecular dynamics simulations suggest pronounced non-native interactions as the origin of the slow escape from this deep trap in the free-energy surface, and a variational enhanced path-sampling approach enables a glimpse of the folding process that is supported by the experimental data.
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Affiliation(s)
- Fabian Dingfelder
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Iuri Macocco
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Stephan Benke
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pietro Faccioli
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- INFN-TIFPA, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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11
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Spoel D, Zhang J, Zhang H. Quantitative predictions from molecular simulations using explicit or implicit interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1560] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- David Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology Uppsala University Uppsala Sweden
| | - Jin Zhang
- Department of Chemistry Southern University of Science and Technology Shenzhen China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing China
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12
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Zhang J, Ye S, Zhong K, Zhang Y, Chong Y, Zhao L, Zhou H, Guo S, Zhang G, Jiang B, Mukamel S, Jiang J. A Machine-Learning Protocol for Ultraviolet Protein-Backbone Absorption Spectroscopy under Environmental Fluctuations. J Phys Chem B 2021; 125:6171-6178. [PMID: 34086461 DOI: 10.1021/acs.jpcb.1c03296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet (UV) absorption spectra are commonly used for characterizing the global structure of proteins. However, the theoretical interpretation of UV spectra is hindered by the large number of required expensive ab initio calculations of excited states spanning a huge conformation space. We present a machine-learning (ML) protocol for far-UV (FUV) spectra of proteins, which can predict FUV spectra of proteins with comparable accuracy to density functional theory (DFT) calculations but with 3-4 orders of magnitude reduced computational cost. It further shows excellent predictive power and transferability that can be used to probe structural mutations and protein folding pathways.
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Affiliation(s)
- Jinxiao Zhang
- Guangxi Key Laboratory of Electrochemical and Magneto-chemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541006, China
| | - Sheng Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Kai Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yaolong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuanyuan Chong
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Luyuan Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huiting Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Sibei Guo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guozhen Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shaul Mukamel
- Departments of Chemistry and Physics & Astronomy, University of California, Irvine, California 92697, United States
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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13
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Clinger JA, Chen E, Kliger DS, Phillips GN. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. J Phys Chem B 2021; 125:202-210. [PMID: 33355472 DOI: 10.1021/acs.jpcb.0c04822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.
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Affiliation(s)
- Jonathan A Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
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14
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Spagnolli G, Massignan T, Astolfi A, Biggi S, Rigoli M, Brunelli P, Libergoli M, Ianeselli A, Orioli S, Boldrini A, Terruzzi L, Bonaldo V, Maietta G, Lorenzo NL, Fernandez LC, Codeseira YB, Tosatto L, Linsenmeier L, Vignoli B, Petris G, Gasparotto D, Pennuto M, Guella G, Canossa M, Altmeppen HC, Lolli G, Biressi S, Pastor MM, Requena JR, Mancini I, Barreca ML, Faccioli P, Biasini E. Pharmacological inactivation of the prion protein by targeting a folding intermediate. Commun Biol 2021; 4:62. [PMID: 33437023 PMCID: PMC7804251 DOI: 10.1038/s42003-020-01585-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Recent computational advancements in the simulation of biochemical processes allow investigating the mechanisms involved in protein regulation with realistic physics-based models, at an atomistic level of resolution. These techniques allowed us to design a drug discovery approach, named Pharmacological Protein Inactivation by Folding Intermediate Targeting (PPI-FIT), based on the rationale of negatively regulating protein levels by targeting folding intermediates. Here, PPI-FIT was tested for the first time on the cellular prion protein (PrP), a cell surface glycoprotein playing a key role in fatal and transmissible neurodegenerative pathologies known as prion diseases. We predicted the all-atom structure of an intermediate appearing along the folding pathway of PrP and identified four different small molecule ligands for this conformer, all capable of selectively lowering the load of the protein by promoting its degradation. Our data support the notion that the level of target proteins could be modulated by acting on their folding pathways, implying a previously unappreciated role for folding intermediates in the biological regulation of protein expression. Spagnolli, Massignan, Astolfi et al. design a new drug discovery approach, termed Pharmacological Protein Inactivation by Folding Intermediate Targeting, in which folding intermediates of disease-causing proteins are targeted. They test it on the cellular prion protein, identifying ligands stabilizing a folding intermediate and consequently promoting its degradation by the cellular quality control machinery.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Tania Massignan
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy.,Sibylla Biotech SRL, 37121, Verona, VR, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, 06123, Perugia, PG, Italy
| | - Silvia Biggi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Marta Rigoli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Paolo Brunelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Michela Libergoli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Alan Ianeselli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Simone Orioli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy.,INFN-TIFPA, University of Trento, Povo, Trento, TN, Italy
| | - Alberto Boldrini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Sibylla Biotech SRL, 37121, Verona, VR, Italy
| | - Luca Terruzzi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Sibylla Biotech SRL, 37121, Verona, VR, Italy
| | - Valerio Bonaldo
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Giulia Maietta
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Nuria L Lorenzo
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Leticia C Fernandez
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Yaiza B Codeseira
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Laura Tosatto
- Institute of Biophysics, National Council of Research, 38123 Povo, Trento, TN, Italy
| | - Luise Linsenmeier
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Beatrice Vignoli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Gianluca Petris
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy
| | - Dino Gasparotto
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Maria Pennuto
- Department of Biomedical Sciences (DBS), University of Padova, 35131, Padova, Italy.,Veneto Institute of Molecular Medicine (VIMM), 35129, Padova, Italy
| | - Graziano Guella
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Marco Canossa
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy
| | - Hermann C Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy
| | - Stefano Biressi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Manuel M Pastor
- RIAIDT, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Ines Mancini
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Maria L Barreca
- Department of Pharmaceutical Sciences, University of Perugia, 06123, Perugia, PG, Italy.
| | - Pietro Faccioli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy. .,INFN-TIFPA, University of Trento, Povo, Trento, TN, Italy.
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy. .,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy.
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15
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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16
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Terruzzi L, Spagnolli G, Boldrini A, Requena JR, Biasini E, Faccioli P. All-atom simulation of the HET-s prion replication. PLoS Comput Biol 2020; 16:e1007922. [PMID: 32946455 PMCID: PMC7526898 DOI: 10.1371/journal.pcbi.1007922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/30/2020] [Accepted: 08/03/2020] [Indexed: 11/18/2022] Open
Abstract
Prions are self-replicative protein particles lacking nucleic acids. Originally discovered for causing infectious neurodegenerative disorders, they have also been found to play several physiological roles in a variety of species. Functional and pathogenic prions share a common mechanism of replication, characterized by the ability of an amyloid conformer to propagate by inducing the conversion of its physiological, soluble counterpart. Since time-resolved biophysical experiments are currently unable to provide full reconstruction of the physico-chemical mechanisms responsible for prion replication, one must rely on computer simulations. In this work, we show that a recently developed algorithm called Self-Consistent Path Sampling (SCPS) overcomes the computational limitations of plain MD and provides a viable tool to investigate prion replication processes using state-of-the-art all-atom force fields in explicit solvent. First, we validate the reliability of SCPS simulations by characterizing the folding of a class of small proteins and comparing against the results of plain MD simulations. Next, we use SCPS to investigate the replication of the prion forming domain of HET-s, a physiological fungal prion for which high-resolution structural data are available. Our atomistic reconstruction shows remarkable similarities with a previously reported mechanism of mammalian PrPSc propagation obtained using a simpler and more approximate path sampling algorithm. Together, these results suggest that the propagation of prions generated by evolutionary distant proteins may share common features. In particular, in both these cases, prions propagate their conformation through a very similar templating mechanism. Prions are proteins capable of replicating in absence of nucleic acids. By propagating the information encoded in their conformation, prions exemplify the phenomenon of protein-based inheritance. These peculiar agents are associated with neurodegenerative pathologies in mammals, but also involved in a wide variety of physiological processes occurring in various biological contexts along the evolutionary scale. In this work, we apply a recently developed computational method to study the propagation mechanism of the fungal prion HET-s, using a realistic all-atom model. We find that the replication of HET-s shares fundamental features with the templated conversion of the mammalian prion PrPSc.
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Affiliation(s)
- Luca Terruzzi
- Sibylla Biotech SRL, Verona, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy
| | - Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy.,Dulbecco Telethon Institute, University of Trento, Povo, Trento, Italy
| | - Alberto Boldrini
- Sibylla Biotech SRL, Verona, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Spain
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy.,Dulbecco Telethon Institute, University of Trento, Povo, Trento, Italy
| | - Pietro Faccioli
- Department of Physics, University of Trento, Povo, Trento, Italy.,INFN-TIFPA, University of Trento, Povo, Trento, Italy
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17
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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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18
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Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:123-176. [PMID: 32145944 DOI: 10.1016/bs.pmbts.2019.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modeling tool to interpret experimental measurements, and to use experimental data to refine our biophysical models. Thus, explicit integration and synergy between molecular simulations and experiments is fundamental for furthering our understanding of biological processes. This is especially true in the case where discrepancies between measured and simulated observables emerge. In this chapter, we provide an overview of some of the core ideas behind methods that were developed to improve the consistency between experimental information and numerical predictions. We distinguish between situations where experiments are used to refine our understanding and models of specific systems, and situations where experiments are used more generally to refine transferable models. We discuss different philosophies and attempt to unify them in a single framework. Until now, such integration between experiments and simulations have mostly been applied to equilibrium data, and we discuss more recent developments aimed to analyze time-dependent or time-resolved data.
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Affiliation(s)
- Simone Orioli
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Haahr Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Atomistic Simulations Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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19
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Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020; 295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003.
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065, India.
| | - Pietro Faccioli
- Dipartimento di Fisica, Universitá degli Studi di Trento, 38122 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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20
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Rogers DM, Jasim SB, Dyer NT, Auvray F, Réfrégiers M, Hirst JD. Electronic Circular Dichroism Spectroscopy of Proteins. Chem 2019. [DOI: 10.1016/j.chempr.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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The role of circular dichroism spectroscopy in the era of integrative structural biology. Curr Opin Struct Biol 2019; 58:191-196. [DOI: 10.1016/j.sbi.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022]
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22
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Yang L, Xue J, Jia Y, Zhang Y, Wu D, Ma H, Wei Q, Ju H. Construction of well-ordered electrochemiluminescence sensing interface using peptide-based specific antibody immobilizer and N-(aminobutyl)-N-(ethylisoluminol) functionalized ferritin as signal indicator for procalcitonin analysis. Biosens Bioelectron 2019; 142:111562. [DOI: 10.1016/j.bios.2019.111562] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/20/2019] [Accepted: 08/01/2019] [Indexed: 11/16/2022]
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23
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Spagnolli G, Rigoli M, Orioli S, Sevillano AM, Faccioli P, Wille H, Biasini E, Requena JR. Full atomistic model of prion structure and conversion. PLoS Pathog 2019; 15:e1007864. [PMID: 31295325 PMCID: PMC6622554 DOI: 10.1371/journal.ppat.1007864] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/23/2019] [Indexed: 11/19/2022] Open
Abstract
Prions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids. The first prion identified, the scrapie isoform (PrPSc) of the cellular prion protein (PrPC), caused epidemic and epizootic episodes [1]. Most aggregates of other misfolding-prone proteins are amyloids, often arranged in a Parallel-In-Register-β-Sheet (PIRIBS) [2] or β-solenoid conformations [3]. Similar folding models have also been proposed for PrPSc, although none of these have been confirmed experimentally. Recent cryo-electron microscopy (cryo-EM) and X-ray fiber-diffraction studies provided evidence that PrPSc is structured as a 4-rung β-solenoid (4RβS) [4, 5]. Here, we combined different experimental data and computational techniques to build the first physically-plausible, atomic resolution model of mouse PrPSc, based on the 4RβS architecture. The stability of this new PrPSc model, as assessed by Molecular Dynamics (MD) simulations, was found to be comparable to that of the prion forming domain of Het-s, a naturally-occurring β-solenoid. Importantly, the 4RβS arrangement allowed the first simulation of the sequence of events underlying PrPC conversion into PrPSc. This study provides the most updated, experimentally-driven and physically-coherent model of PrPSc, together with an unprecedented reconstruction of the mechanism underlying the self-catalytic propagation of prions.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- * E-mail: (GS); (EB); (JRR)
| | - Marta Rigoli
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- Department of Physics, Povo, Trento TN, ITALY
| | - Simone Orioli
- Department of Physics, Povo, Trento TN, ITALY
- INFN-TIFPA, Povo (Trento), ITALY
| | - Alejandro M. Sevillano
- Department of Pathology–University of California—San Diego, San Diego, California, United States of America
| | - Pietro Faccioli
- Department of Physics, Povo, Trento TN, ITALY
- INFN-TIFPA, Povo (Trento), ITALY
| | - Holger Wille
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases–University of Alberta, Edmonton (AB), CANADA
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO)–University of Trento, Povo TN, ITALY
- * E-mail: (GS); (EB); (JRR)
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago, SPAIN
- * E-mail: (GS); (EB); (JRR)
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24
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Michaelis M, Hildebrand N, Meißner RH, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Delle Piane M, Colombi Ciacchi L. Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. J Phys Chem B 2019; 123:6694-6704. [DOI: 10.1021/acs.jpcb.9b03932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- M. Michaelis
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - N. Hildebrand
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - R. H. Meißner
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - N. Wurzler
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Z. Li
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - J. D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - A. Micsonai
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - J. Kardos
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - M. Delle Piane
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - L. Colombi Ciacchi
- Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, Hybrid Materials Interfaces Group, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
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25
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Yang Y, Wang R, Feng W, Zhou X, Chen Z, Wang T. Carboxymethylcellulose/pectin inhibiting structural folding of rice proteins via trinary structural interplays. Int J Biol Macromol 2019; 133:93-100. [DOI: 10.1016/j.ijbiomac.2019.04.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/31/2022]
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Gendron F, Moore Ii B, Cador O, Pointillart F, Autschbach J, Le Guennic B. Ab Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-Allowed and Spin-Forbidden Transitions: From Organic Ketones to Lanthanide Complexes. J Chem Theory Comput 2019; 15:4140-4155. [PMID: 31125219 DOI: 10.1021/acs.jctc.9b00286] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wave function methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral cobalt(III) complex [Co(en)3]3+, and the europium(III) complex [Eu(DPA)3]3-. The ab initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab initio for the spin-forbidden transitions of both a transition metal and a lanthanide complex.
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Affiliation(s)
- Frédéric Gendron
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Barry Moore Ii
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Olivier Cador
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Fabrice Pointillart
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Jochen Autschbach
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Boris Le Guennic
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
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Wang F, Orioli S, Ianeselli A, Spagnolli G, A Beccara S, Gershenson A, Faccioli P, Wintrode PL. All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding. Biophys J 2019; 114:2083-2094. [PMID: 29742402 DOI: 10.1016/j.bpj.2018.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022] Open
Abstract
Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α1-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α1-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, whereas the relatively benign S mutant shows late-stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation, and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.
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Affiliation(s)
- Fang Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Simone Orioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Alan Ianeselli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Giovanni Spagnolli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Silvio A Beccara
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts.
| | - Pietro Faccioli
- Dipartimento di Fisica, Università degli Studi di Trento, Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland.
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Yang L, Fan D, Zhang Y, Ding C, Wu D, Wei Q, Ju H. Ferritin-Based Electrochemiluminescence Nanosurface Energy Transfer System for Procalcitonin Detection Using HWRGWVC Heptapeptide for Site-Oriented Antibody Immobilization. Anal Chem 2019; 91:7145-7152. [DOI: 10.1021/acs.analchem.9b00325] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lei Yang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Dawei Fan
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Yong Zhang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Dan Wu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Huangxian Ju
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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