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Bakker MJ, Gaffour A, Juhás M, Zapletal V, Stošek J, Bratholm LA, Pavlíková Přecechtělová J. Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering. J Chem Inf Model 2024; 64:6542-6556. [PMID: 39099394 DOI: 10.1021/acs.jcim.4c00809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
By merging advanced dimensionality reduction (DR) and clustering algorithm (CA) techniques, our study advances the sampling procedure for predicting NMR chemical shifts (CS) in intrinsically disordered proteins (IDPs), making a significant leap forward in the field of protein analysis/modeling. We enhance NMR CS sampling by generating clustered ensembles that accurately reflect the different properties and phenomena encapsulated by the IDP trajectories. This investigation critically assessed different rapid CS predictors, both neural network (e.g., Sparta+ and ShiftX2) and database-driven (ProCS-15), and highlighted the need for more advanced quantum calculations and the subsequent need for more tractable-sized conformational ensembles. Although neural network CS predictors outperformed ProCS-15 for all atoms, all tools showed poor agreement with HN CSs, and the neural network CS predictors were unable to capture the influence of phosphorylated residues, highly relevant for IDPs. This study also addressed the limitations of using direct clustering with collective variables, such as the widespread implementation of the GROMOS algorithm. Clustered ensembles (CEs) produced by this algorithm showed poor performance with chemical shifts compared to sequential ensembles (SEs) of similar size. Instead, we implement a multiscale DR and CA approach and explore the challenges and limitations of applying these algorithms to obtain more robust and tractable CEs. The novel feature of this investigation is the use of solvent-accessible surface area (SASA) as one of the fingerprints for DR alongside previously investigated α carbon distance/angles or ϕ/ψ dihedral angles. The ensembles produced with SASA tSNE DR produced CEs better aligned with the experimental CS of between 0.17 and 0.36 r2 (0.18-0.26 ppm) depending on the system and replicate. Furthermore, this technique produced CEs with better agreement than traditional SEs in 85.7% of all ensemble sizes. This study investigates the quality of ensembles produced based on different input features, comparing latent spaces produced by linear vs nonlinear DR techniques and a novel integrated silhouette score scanning protocol for tSNE DR.
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Affiliation(s)
- Michael J Bakker
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Amina Gaffour
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Martin Juhás
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Rokitanského 62, 500 03 Hradec Králové, Czech Republic
| | - Vojtěch Zapletal
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Jakub Stošek
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lars A Bratholm
- School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS Bristol, U.K
| | - Jana Pavlíková Přecechtělová
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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Ribeiro IC, de Moraes JVB, Mariotini-Moura C, Polêto MD, da Rocha Torres Pavione N, de Castro RB, Miranda IL, Sartori SK, Alves KLS, Bressan GC, de Souza Vasconcellos R, Meyer-Fernandes JR, Diaz-Muñoz G, Fietto JLR. Synthesis of new non-natural L-glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate diphosphohydrolase 1 (TcNTPDase1). Purinergic Signal 2024; 20:399-419. [PMID: 37975950 PMCID: PMC11303637 DOI: 10.1007/s11302-023-09974-7] [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: 05/03/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Trypanosoma cruzi is the pathogen of Chagas disease, a neglected tropical disease that affects more than 6 million people worldwide. There are no vaccines to prevent infection, and the therapeutic arsenal is very minimal and toxic. The unique E-NTPDase of T. cruzi (TcNTPDase1) plays essential roles in adhesion and infection and is a virulence factor. Quercetin is a flavonoid with antimicrobial, antiviral, and antitumor activities. Its potential as a partial inhibitor of NTPDases has also been demonstrated. In this work, we synthesized the non-natural L-glycoside derivatives of quercetin and evaluated them as inhibitors of recombinant TcNTPDase1 (rTcNTPDase1). These compounds, and quercetin and miquelianin, a natural quercetin derivative, were also tested. Compound 16 showed the most significant inhibitory effect (94%). Quercetin, miquelianin, and compound 14 showed inhibition close to 50%. We thoroughly investigated the inhibitory effect of 16. Our data suggested a competitive inhibition with a Ki of 8.39 μM (± 0.90). To better understand the interaction of compound 16 and rTcNTPDase1, we performed molecular dynamics simulations of the enzyme and docking analyses with the compounds. Our predictions show that compound 16 binds to the enzyme's catalytic site and interacts with important residues for NTPDase activity. As an inhibitor of a critical T. cruzi enzyme, (16) could be helpful as a starting point in the developing of a future treatment for Chagas disease. Furthermore, the discovery of (16) as an inhibitor of TcNTPDase1 may open new avenues in the study and development of new inhibitors of E-NTPDases.
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Affiliation(s)
- Isadora Cunha Ribeiro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Christiane Mariotini-Moura
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Medicine and Nursing Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcelo Depolo Polêto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Raissa Barbosa de Castro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Izabel Luzia Miranda
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Suélen Karine Sartori
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kryssia Lohayne Santos Alves
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo Costa Bressan
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - José Roberto Meyer-Fernandes
- Laboratory of Cellular Biochemistry, Institute of Medical Biochemistry Leopoldo de Meis, Health Sciences Center, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gaspar Diaz-Muñoz
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Juliana Lopes Rangel Fietto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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3
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Zhang Z, Gehin C, Abriata LA, Dal Peraro M, Lashuel H. Differential Effects of Post-translational Modifications on the Membrane Interaction of Huntingtin Protein. ACS Chem Neurosci 2024; 15:2408-2419. [PMID: 38752226 PMCID: PMC11191595 DOI: 10.1021/acschemneuro.4c00091] [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: 02/07/2024] [Revised: 04/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Huntington's disease is a neurodegenerative disorder caused by an expanded polyglutamine stretch near the N-terminus of the huntingtin (HTT) protein, rendering the protein more prone to aggregate. The first 17 residues in HTT (Nt17) interact with lipid membranes and harbor multiple post-translational modifications (PTMs) that can modulate HTT conformation and aggregation. In this study, we used a combination of biophysical studies and molecular simulations to investigate the effect of PTMs on the helicity of Nt17 in the presence of various lipid membranes. We demonstrate that anionic lipids such as PI4P, PI(4,5)P2, and GM1 significantly enhance the helical structure of unmodified Nt17. This effect is attenuated by single acetylation events at K6, K9, or K15, whereas tri-acetylation at these sites abolishes Nt17-membrane interaction. Similarly, single phosphorylation at S13 and S16 decreased but did not abolish the POPG and PIP2-induced helicity, while dual phosphorylation at these sites markedly diminished Nt17 helicity, regardless of lipid composition. The helicity of Nt17 with phosphorylation at T3 is insensitive to the membrane environment. Oxidation at M8 variably affects membrane-induced helicity, highlighting a lipid-dependent modulation of the Nt17 structure. Altogether, our findings reveal differential effects of PTMs and crosstalks between PTMs on membrane interaction and conformation of HTT. Intriguingly, the effects of phosphorylation at T3 or single acetylation at K6, K9, and K15 on Nt17 conformation in the presence of certain membranes do not mirror that observed in the absence of membranes. Our studies provide novel insights into the complex relationship between Nt17 structure, PTMs, and membrane binding.
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Affiliation(s)
- Zhidian Zhang
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, School of
Life Sciences, Institute of Bioengineering,
Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Laboratory
for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Charlotte Gehin
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, School of
Life Sciences, Institute of Bioengineering,
Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Luciano A Abriata
- Laboratory
for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Laboratory
for Biomolecular Modeling, School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale
de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Hilal Lashuel
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, School of
Life Sciences, Institute of Bioengineering,
Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
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Krapp LF, Abriata LA, Cortés Rodriguez F, Dal Peraro M. PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces. Nat Commun 2023; 14:2175. [PMID: 37072397 PMCID: PMC10113261 DOI: 10.1038/s41467-023-37701-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Proteins are essential molecular building blocks of life, responsible for most biological functions as a result of their specific molecular interactions. However, predicting their binding interfaces remains a challenge. In this study, we present a geometric transformer that acts directly on atomic coordinates labeled only with element names. The resulting model-the Protein Structure Transformer, PeSTo-surpasses the current state of the art in predicting protein-protein interfaces and can also predict and differentiate between interfaces involving nucleic acids, lipids, ions, and small molecules with high confidence. Its low computational cost enables processing high volumes of structural data, such as molecular dynamics ensembles allowing for the discovery of interfaces that remain otherwise inconspicuous in static experimentally solved structures. Moreover, the growing foldome provided by de novo structural predictions can be easily analyzed, providing new opportunities to uncover unexplored biology.
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Affiliation(s)
- Lucien F Krapp
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Fabio Cortés Rodriguez
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland.
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5
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Klem H, Hocky GM, McCullagh M. Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories. J Chem Theory Comput 2022; 18:3218-3230. [PMID: 35483073 DOI: 10.1021/acs.jctc.1c01290] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the innate rotational and translational invariance of these features. The vast number of possible internal coordinates necessitates a feature space supervision step to make clustering tractable but yields a protocol that can be system type-specific. Particle positions offer an appealing alternative to internal coordinates but suffer from a lack of rotational and translational invariance, as well as a perceived insensitivity to regions of structural dissimilarity. Here, we present a method, denoted shape-GMM, that overcomes the shortcomings of particle positions using a weighted maximum likelihood alignment procedure. This alignment strategy is then built into an expectation maximization Gaussian mixture model (GMM) procedure to capture metastable states in the free-energy landscape. The resulting algorithm distinguishes between a variety of different structures, including those indistinguishable by root-mean-square displacement and pairwise distances, as demonstrated on several model systems. Shape-GMM results on an extensive simulation of the fast-folding HP35 Nle/Nle mutant protein support a four-state folding/unfolding mechanism, which is consistent with previous experimental results and provides kinetic details comparable to previous state-of-the art clustering approaches, as measured by the VAMP-2 score. Currently, training of shape-GMMs is recommended for systems (or subsystems) that can be represented by ≲200 particles and ≲100k configurations to estimate high-dimensional covariance matrices and balance computational expense. Once a shape-GMM is trained, it can be used to predict the cluster identities of millions of configurations.
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Affiliation(s)
- Heidi Klem
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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Platero-Rochart D, González-Alemán R, Hernández-Rodríguez EW, Leclerc F, Caballero J, Montero-Cabrera L. RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics. Bioinformatics 2022; 38:1863-1869. [PMID: 35020783 DOI: 10.1093/bioinformatics/btac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/06/2021] [Accepted: 01/07/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Density Peaks is a widely spread clustering algorithm that has been previously applied to Molecular Dynamics (MD) simulations. Its conception of cluster centers as elements displaying both a high density of neighbors and a large distance to other elements of high density, particularly fits the nature of a geometrical converged MD simulation. Despite its theoretical convenience, implementations of Density Peaks carry a quadratic memory complexity that only permits the analysis of relatively short trajectories. RESULTS Here, we describe DP+, an exact novel implementation of Density Peaks that drastically reduces the RAM consumption in comparison to the scarcely available alternatives designed for MD. Based on DP+, we developed RCDPeaks, a refined variant of the original Density Peaks algorithm. Through the use of DP+, RCDPeaks was able to cluster a one-million frames trajectory using less than 4.5 GB of RAM, a task that would have taken more than 2 TB and about 3× more time with the fastest and less memory-hunger alternative currently available. Other key features of RCDPeaks include the automatic selection of parameters, the screening of center candidates and the geometrical refining of returned clusters. AVAILABILITY AND IMPLEMENTATION The source code and documentation of RCDPeaks are free and publicly available on GitHub (https://github.com/LQCT/RCDPeaks.git). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Platero-Rochart
- Departamento de Química-Física, Laboratorio de Química Computacional y Teórica (LQCT), Facultad de Química, Universidad de La Habana, La Habana 10400, Cuba
| | - Roy González-Alemán
- Departamento de Química-Física, Laboratorio de Química Computacional y Teórica (LQCT), Facultad de Química, Universidad de La Habana, La Habana 10400, Cuba.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette F-91198, France
| | - Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional (LBQC), Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile.,Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette F-91198, France
| | - Julio Caballero
- Departamento de Bioinformática, Facultad de Ingeniería, Centro de Bioinformática, Simulación y Modelado (CBSM), Universidad de Talca, Talca 3460000, Chile
| | - Luis Montero-Cabrera
- Departamento de Química-Física, Laboratorio de Química Computacional y Teórica (LQCT), Facultad de Química, Universidad de La Habana, La Habana 10400, Cuba
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Damjanovic J, Murphy JM, Lin YS. CATBOSS: Cluster Analysis of Trajectories Based on Segment Splitting. J Chem Inf Model 2021; 61:5066-5081. [PMID: 34608796 PMCID: PMC8549068 DOI: 10.1021/acs.jcim.1c00598] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Molecular dynamics
(MD) simulations are an exceedingly and increasingly
potent tool for molecular behavior prediction and analysis. However,
the enormous wealth of data generated by these simulations can be
difficult to process and render in a human-readable fashion. Cluster
analysis is a commonly used way to partition data into structurally
distinct states. We present a method that improves on the state of
the art by taking advantage of the temporal information of MD trajectories
to enable more accurate clustering at a lower memory cost. To date,
cluster analysis of MD simulations has generally treated simulation
snapshots as a mere collection of independent data points and attempted
to separate them into different clusters based on structural similarity.
This new method, cluster analysis of trajectories based on segment
splitting (CATBOSS), applies density-peak-based clustering to classify trajectory segments learned by change detection. Applying
the method to a synthetic toy model as well as four real-life data
sets–trajectories of MD simulations of alanine dipeptide and
valine dipeptide as well as two fast-folding proteins–we find
CATBOSS to be robust and highly performant, yielding natural-looking
cluster boundaries and greatly improving clustering resolution. As
the classification of points into segments emphasizes density gaps
in the data by grouping them close to the state means, CATBOSS applied
to the valine dipeptide system is even able to account for a degree
of freedom deliberately omitted from the input data set. We also demonstrate
the potential utility of CATBOSS in distinguishing metastable states
from transition segments as well as promising application to cases
where there is little or no advance knowledge of intrinsic coordinates,
making for a highly versatile analysis tool.
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Affiliation(s)
- Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - James M Murphy
- Department of Mathematics, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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