1
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Li SS, Liu ZM, Li J, Ma YB, Dong ZY, Hou JW, Shen FJ, Wang WB, Li QM, Su JG. Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method. BMC Bioinformatics 2024; 25:282. [PMID: 39198740 PMCID: PMC11360314 DOI: 10.1186/s12859-024-05876-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND Thermostability is a fundamental property of proteins to maintain their biological functions. Predicting protein stability changes upon mutation is important for our understanding protein structure-function relationship, and is also of great interest in protein engineering and pharmaceutical design. RESULTS Here we present mutDDG-SSM, a deep learning-based framework that uses the geometric representations encoded in protein structure to predict the mutation-induced protein stability changes. mutDDG-SSM consists of two parts: a graph attention network-based protein structural feature extractor that is trained with a self-supervised learning scheme using large-scale high-resolution protein structures, and an eXtreme Gradient Boosting model-based stability change predictor with an advantage of alleviating overfitting problem. The performance of mutDDG-SSM was tested on several widely-used independent datasets. Then, myoglobin and p53 were used as case studies to illustrate the effectiveness of the model in predicting protein stability changes upon mutations. Our results show that mutDDG-SSM achieved high performance in estimating the effects of mutations on protein stability. In addition, mutDDG-SSM exhibited good unbiasedness, where the prediction accuracy on the inverse mutations is as well as that on the direct mutations. CONCLUSION Meaningful features can be extracted from our pre-trained model to build downstream tasks and our model may serve as a valuable tool for protein engineering and drug design.
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Affiliation(s)
- Shan Shan Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Zhao Ming Liu
- National Engineering Center for New Vaccine Research, Beijing, China
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Jiao Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Yi Bo Ma
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Yuan Dong
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Jun Wei Hou
- National Engineering Center for New Vaccine Research, Beijing, China
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Fu Jie Shen
- National Engineering Center for New Vaccine Research, Beijing, China
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Wei Bu Wang
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China
- National Engineering Center for New Vaccine Research, Beijing, China
| | - Qi Ming Li
- National Engineering Center for New Vaccine Research, Beijing, China.
- The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China.
| | - Ji Guo Su
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China.
- National Engineering Center for New Vaccine Research, Beijing, China.
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2
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Martinez-Martin I, Crousilles A, Ochoa JP, Velazquez-Carreras D, Mortensen SA, Herrero-Galan E, Delgado J, Dominguez F, Garcia-Pavia P, de Sancho D, Wilmanns M, Alegre-Cebollada J. Titin domains with reduced core hydrophobicity cause dilated cardiomyopathy. Cell Rep 2023; 42:113490. [PMID: 38052212 DOI: 10.1016/j.celrep.2023.113490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The underlying genetic defect in most cases of dilated cardiomyopathy (DCM), a common inherited heart disease, remains unknown. Intriguingly, many patients carry single missense variants of uncertain pathogenicity targeting the giant protein titin, a fundamental sarcomere component. To explore the deleterious potential of these variants, we first solved the wild-type and mutant crystal structures of I21, the titin domain targeted by pathogenic variant p.C3575S. Although both structures are remarkably similar, the reduced hydrophobicity of deeply buried position 3575 strongly destabilizes the mutant domain, a scenario supported by molecular dynamics simulations and by biochemical assays that show no disulfide involving C3575. Prompted by these observations, we have found that thousands of similar hydrophobicity-reducing variants associate specifically with DCM. Hence, our results imply that titin domain destabilization causes DCM, a conceptual framework that not only informs pathogenicity assessment of gene variants but also points to therapeutic strategies counterbalancing protein destabilization.
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Affiliation(s)
- Ines Martinez-Martin
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain.
| | - Audrey Crousilles
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Juan Pablo Ochoa
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, CIBERCV, 28222 Madrid, Spain; Health in Code, 15008 A Coruña, Spain
| | | | - Simon A Mortensen
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Elias Herrero-Galan
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Javier Delgado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Fernando Dominguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, CIBERCV, 28222 Madrid, Spain
| | - Pablo Garcia-Pavia
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Heart Failure and Inherited Cardiac Diseases Unit, Department of Cardiology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, CIBERCV, 28222 Madrid, Spain
| | - David de Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU, 20018 Donostia-San Sebastian, Euskadi, Spain; Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastian, Euskadi, Spain
| | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
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3
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Breznik M, Ge Y, Bluck JP, Briem H, Hahn DF, Christ CD, Mortier J, Mobley DL, Meier K. Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods. ChemMedChem 2023; 18:e202200425. [PMID: 36240514 PMCID: PMC9868080 DOI: 10.1002/cmdc.202200425] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Indexed: 01/26/2023]
Abstract
Prioritizing molecules for synthesis is a key role of computational methods within medicinal chemistry. Multiple tools exist for ranking molecules, from the cheap and popular molecular docking methods to more computationally expensive molecular-dynamics (MD)-based methods. It is often questioned whether the accuracy of the more rigorous methods justifies the higher computational cost and associated calculation time. Here, we compared the performance on ranking the binding of small molecules for seven scoring functions from five docking programs, one end-point method (MM/GBSA), and two MD-based free energy methods (PMX, FEP+). We investigated 16 pharmaceutically relevant targets with a total of 423 known binders. The performance of docking methods for ligand ranking was strongly system dependent. We observed that MD-based methods predominantly outperformed docking algorithms and MM/GBSA calculations. Based on our results, we recommend the application of MD-based free energy methods for prioritization of molecules for synthesis in lead optimization, whenever feasible.
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Affiliation(s)
- Marko Breznik
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Joseph P. Bluck
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Hans Briem
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Clara D. Christ
- Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Jérémie Mortier
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA,Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Katharina Meier
- Computational Life Science Technology Functions, Crop Science, R&D, Bayer AG, 40789 Monheim, Germany
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4
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Jackson V, Hermann J, Tynan CJ, Rolfe DJ, Corey RA, Duncan AL, Noriega M, Chu A, Kalli AC, Jones EY, Sansom MSP, Martin-Fernandez ML, Seiradake E, Chavent M. The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X 3-small transmembrane motifs. Structure 2022; 30:1354-1365.e5. [PMID: 35700726 DOI: 10.1016/j.str.2022.05.014] [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: 08/02/2021] [Revised: 03/03/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Fibronectin Leucine-rich Repeat Transmembrane (FLRT 1-3) proteins are a family of broadly expressed single-spanning transmembrane receptors that play key roles in development. Their extracellular domains mediate homotypic cell-cell adhesion and heterotypic protein interactions with other receptors to regulate cell adhesion and guidance. These in trans FLRT interactions determine the formation of signaling complexes of varying complexity and function. Whether FLRTs also interact at the surface of the same cell, in cis, remains unknown. Here, molecular dynamics simulations reveal two dimerization motifs in the FLRT2 transmembrane helix. Single particle tracking experiments show that these Small-X3-Small motifs synergize with a third dimerization motif encoded in the extracellular domain to permit the cis association and co-diffusion patterns of FLRT2 receptors on cells. These results may point to a competitive switching mechanism between in cis and in trans interactions, which suggests that homotypic FLRT interaction mirrors the functionalities of classic adhesion molecules.
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Affiliation(s)
- Verity Jackson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Julia Hermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Christopher J Tynan
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Daniel J Rolfe
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Maxime Noriega
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Amy Chu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, LS2 9NL, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Campus, Didcot, OX11 0FA, UK.
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France.
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5
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Jespers W, Isaksen GV, Andberg TA, Vasile S, van Veen A, Åqvist J, Brandsdal BO, Gutiérrez-de-Terán H. QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q. J Chem Theory Comput 2019; 15:5461-5473. [DOI: 10.1021/acs.jctc.9b00538] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 590, S-75124 Uppsala, Sweden
| | - Geir V. Isaksen
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 590, S-75124 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø−The Arctic University of Norway, N9037 Tromsø, Norway
| | - Tor A.H. Andberg
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø−The Arctic University of Norway, N9037 Tromsø, Norway
| | - Silvana Vasile
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 590, S-75124 Uppsala, Sweden
| | - Amber van Veen
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 590, S-75124 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 590, S-75124 Uppsala, Sweden
| | - Bjørn Olav Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø−The Arctic University of Norway, N9037 Tromsø, Norway
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 590, S-75124 Uppsala, Sweden
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6
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Sahoo A, Matysiak S. Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration. Phys Chem Chem Phys 2019; 21:22679-22694. [DOI: 10.1039/c9cp02765c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An overview of recent advances in computational investigation of peptide–lipid interactions in neurodegeneration – Alzheimer's, Parkinson's and Huntington's disease.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program
- Institute of Physical Science and Technology
- University of Maryland
- College Park
- USA
| | - Silvina Matysiak
- Biophysics Program
- Institute of Physical Science and Technology
- University of Maryland
- College Park
- USA
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7
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Bochicchio A, Krepl M, Yang F, Varani G, Sponer J, Carloni P. Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. PLoS Comput Biol 2018; 14:e1006642. [PMID: 30521520 PMCID: PMC6307825 DOI: 10.1371/journal.pcbi.1006642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/27/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox·pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations. Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement. RNA is an outstanding target for oncological intervention. Engineering the most common RNA binding motif in human proteins (called RRM) so as to bind to a specific RNA has an enormous pharmacological potential. Yet, it is highly non trivial to design RRM-bearing protein variants with RNA selectivity and affinity sufficiently high for clinical applications. Here we present an extensive molecular simulation study which shed light on the exquisite molecular recognition of the empirically-engineered complex between the RRM-bearing protein Rbfox and its RNA target pre-miR21. The simulations allow predicting a variant, the S151T, which may lead to further enhancement of selectivity and affinity for pre-miR21.
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Affiliation(s)
- Anna Bochicchio
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- * E-mail: (MK); (PC)
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czech Republic
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (MK); (PC)
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8
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Carballo-Pacheco M, Ismail AE, Strodel B. On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6063-6075. [PMID: 30336669 DOI: 10.1021/acs.jctc.8b00579] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ16-22 peptide and two of its mutants: Aβ16-22(F19V,F20V), which does not form fibrils, and Aβ16-22(F19L) which forms fibrils faster than the wild type. We observe that while oligomer formation kinetics depends strongly on the force field, structural properties, such as the most relevant protein-protein contacts, are similar between them. The oligomer formation kinetics obtained with different force fields differ more from each other than the kinetics between aggregating and nonaggregating peptides simulated with a single force field. We discuss the difficulties in comparing atomistic simulations of amyloid oligomer formation with experimental observables.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Ahmed E Ismail
- AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany.,Aachener Verfahrenstechnik, Faculty of Mechanical Engineering , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , 40225 Düsseldorf , Germany
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9
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Markthaler D, Kraus H, Hansen N. Overcoming Convergence Issues in Free-Energy Calculations of Amide-to-Ester Mutations in the Pin1-WW Domain. J Chem Inf Model 2018; 58:2305-2318. [DOI: 10.1021/acs.jcim.8b00581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Markthaler
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Hamzeh Kraus
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
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10
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Lombardo S, Chen P, Larsson PA, Thielemans W, Wohlert J, Svagan AJ. Toward Improved Understanding of the Interactions between Poorly Soluble Drugs and Cellulose Nanofibers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5464-5473. [PMID: 29715039 DOI: 10.1021/acs.langmuir.8b00531] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Cellulose nanofibers (CNFs) have interesting physicochemical and colloidal properties that have been recently exploited in novel drug-delivery systems for tailored release of poorly soluble drugs. The morphology and release kinetics of such drug-delivery systems heavily relied on the drug-CNF interactions; however, in-depth understanding of the interactions was lacking. Herein, the interactions between a poorly soluble model drug molecule, furosemide, and cationic cellulose nanofibers with two different degrees of substitution are studied by sorption experiments, Fourier transform infrared spectroscopy, and molecular dynamics (MD) simulation. Both MD simulations and experimental results confirmed the spontaneous sorption of drug onto CNF. Simulations further showed that adsorption occurred by the flat aryl ring of furosemide. The spontaneous sorption was commensurate with large entropy gains as a result of release of surface-bound water. Association between furosemide molecules furthermore enabled surface precipitation as indicated by both simulations and experiments. Finally, sorption was also found not to be driven by charge neutralization, between positive CNF surface charges and the furosemide negative charge, so that surface area is the single most important parameter determining the amount of sorbed drug. An optimized CNF-furosemide drug-delivery vehicle thus needs to have a maximized specific surface area irrespective of the surface charge with which it is achieved. The findings also provide important insights into the design principles of CNF-based filters suitable for removal of poorly soluble drugs from wastewater.
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Affiliation(s)
- Salvatore Lombardo
- Renewable Materials and Nanotechnology Research Group, Department of Chemical Engineering , KU Leuven , Campus Kulak Kortrijk, Etienne Sabbelaan 53 , P.O. Box 7659, 8500 Kortrijk , Belgium
| | - Pan Chen
- Wallenberg Wood Science Center , KTH , Teknikringen 58 , SE-100 44 Stockholm , Sweden
| | - Per A Larsson
- Fibre and Polymer Technology , KTH Royal Institute of Technology , Teknikringen 56-58 , SE-100 44 Stockholm , Sweden
| | - Wim Thielemans
- Renewable Materials and Nanotechnology Research Group, Department of Chemical Engineering , KU Leuven , Campus Kulak Kortrijk, Etienne Sabbelaan 53 , P.O. Box 7659, 8500 Kortrijk , Belgium
| | - Jakob Wohlert
- Fibre and Polymer Technology , KTH Royal Institute of Technology , Teknikringen 56-58 , SE-100 44 Stockholm , Sweden
| | - Anna J Svagan
- Wallenberg Wood Science Center , KTH , Teknikringen 58 , SE-100 44 Stockholm , Sweden
- Fibre and Polymer Technology , KTH Royal Institute of Technology , Teknikringen 56-58 , SE-100 44 Stockholm , Sweden
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11
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Cortés Cabrera Á, Sánchez-Murcia PA, Gago F. Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations. Phys Chem Chem Phys 2018; 19:23239-23246. [PMID: 28825743 DOI: 10.1039/c7cp03659k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioredoxin (Trx), a small and globular protein, is present in all kinds of organisms, from Archea to higher mammals. Throughout evolution, the Trx sequence has undergone subtle modifications to adapt to varying environmental conditions. The high degree of sequence conservation makes Trx very amenable to ancestral protein reconstruction techniques. In this work, we address the study of the structural and energetic determinants of thermostability in E. coli Trx using a dataset of mutations inspired by ancestral reconstruction. We compute, from first principles, the expected contribution of 19 different amino acid substitutions to the stability (ΔΔG) and the melting temperature (ΔTm) of the protein. We also describe the specific changes in structure and protein dynamics responsible for the stabilizing or destabilizing effects of these mutations. Our results point to local and independent changes for most of the variants. Our predictions are accurate enough to substantiate the proposal of new hypotheses regarding evolutionary relationships between mutations, as in the case of T89R, P68A and G74S or K90L and F102A, and reach beyond the initial set to suggest improved variants, such as K90I or K90Y.
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Affiliation(s)
- Álvaro Cortés Cabrera
- Área de Farmacología, Departamento de Ciencias Biomédicas, Facultad de Medicina y Ciencias de la Salud, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.
| | - Pedro A Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Facultad de Medicina y Ciencias de la Salud, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Facultad de Medicina y Ciencias de la Salud, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.
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12
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Fowler PW, Cole K, Gordon NC, Kearns AM, Llewelyn MJ, Peto TEA, Crook DW, Walker AS. Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus. Cell Chem Biol 2018; 25:339-349.e4. [PMID: 29307840 DOI: 10.1016/j.chembiol.2017.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/24/2017] [Accepted: 12/08/2017] [Indexed: 01/28/2023]
Abstract
The rise of antibiotic resistance threatens modern medicine; to combat it new diagnostic methods are required. Sequencing the whole genome of a pathogen offers the potential to accurately determine which antibiotics will be effective to treat a patient. A key limitation of this approach is that it cannot classify rare or previously unseen mutations. Here we demonstrate that alchemical free energy methods, a well-established class of methods from computational chemistry, can successfully predict whether mutations in Staphylococcus aureus dihydrofolate reductase confer resistance to trimethoprim. We also show that the method is quantitatively accurate by calculating how much the most common resistance-conferring mutation, F99Y, reduces the binding free energy of trimethoprim and comparing predicted and experimentally measured minimum inhibitory concentrations for seven different mutations. Finally, by considering up to 32 free energy calculations for each mutation, we estimate its specificity and sensitivity.
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Affiliation(s)
- Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK.
| | - Kevin Cole
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, Brighton and Sussex Medical School, Brighton BN1 9PS, UK
| | - N Claire Gordon
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - Angela M Kearns
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale NW9 5EQ, UK
| | - Martin J Llewelyn
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, Brighton and Sussex Medical School, Brighton BN1 9PS, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
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Gapsys V, de Groot BL. pmx Webserver: A User Friendly Interface for Alchemistry. J Chem Inf Model 2017; 57:109-114. [DOI: 10.1021/acs.jcim.6b00498] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular
Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Bert L. de Groot
- Computational Biomolecular
Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
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