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Plazinski W, Lutsyk V, Plazinska A. Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field. J Chem Theory Comput 2024; 20:2273-2283. [PMID: 38427574 PMCID: PMC10938637 DOI: 10.1021/acs.jctc.3c01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
Coarse-grained (CG) level molecular dynamics simulations are routinely used to study various biomolecular processes. The Martini force field is currently the most widely adopted parameter set for such simulations. The functional form of this and several other CG force fields enforces secondary protein structure support by employing a variety of harmonic potentials or restraints that favor the protein's native conformation. We propose a straightforward method to calculate the energetic consequences of transitions between predefined conformational states in systems in which multiple factors can affect protein conformational equilibria. This method is designed for use within the Martini force field and involves imposing conformational transitions by linking a Martini-inherent elastic network to the coupling parameter λ. We demonstrate the applicability of our method using the example of five biomolecular systems that undergo experimentally characterized conformational transitions between well-defined structures (Staphylococcal nuclease, C-terminal segment of surfactant protein B, LAH4 peptide, and β2-adrenergic receptor) as well as between folded and unfolded states (GCN4 leucine zipper protein). The results show that the relative free energy changes associated with protein conformational transitions, which are affected by various factors, such as pH, mutations, solvent, and lipid membrane composition, are correctly reproduced. The proposed method may be a valuable tool for understanding how different conditions and modifications affect conformational equilibria in proteins.
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Affiliation(s)
- Wojciech Plazinski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow 30-239, Poland
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, Lublin 20-093, Poland
| | - Valery Lutsyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow 30-239, Poland
| | - Anita Plazinska
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, Lublin 20-093, Poland
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Kapur B, Baldessari F, Lazaratos M, Nar H, Schnapp G, Giorgetti A, Bondar AN. Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68. Comput Struct Biotechnol J 2023; 21:4370-4384. [PMID: 37711190 PMCID: PMC10498176 DOI: 10.1016/j.csbj.2023.08.034] [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: 05/05/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Proton-sensing G Protein Coupled Receptors (GPCRs) sense changes in the extracellular pH to effect cell signaling for cellular homeostasis. They tend to be overexpressed in solid tumors associated with acidic extracellular pH, and are of direct interest as drug targets. How proton-sensing GPCRs sense extracellular acidification and activate upon protonation change is important to understand, because it may guide the design of therapeutics. Lack of publicly available experimental structures make it challenging to discriminate between conflicting mechanisms proposed for proton-binding, as main roles have been assigned to either an extracellular histidine cluster or to an internal carboxylic triad. Here we present a protocol to derive and evaluate structural models of the proton-sensing GPR68. This approach integrates state-of-the-art homology modeling with microsecond-timescale atomistic simulations, and with a detailed assessment of the compatibility of the structural models with known structural features of class A GPCRs. To decipher structural elements of potential interest for protonation-coupled conformational changes of GPR68, we used the best-compatible model as a starting point for independent atomistic simulations of GPR68 with different protonation states, and graph computations to characterize the response of GPR68 to changes in protonation. We found that GPR68 hosts an extended hydrogen-bond network that inter-connects the extracellular histidine cluster to the internal carboxylic triad, and which can even reach groups at the cytoplasmic G-protein binding site. Taken together, results suggest that GPR68 relies on dynamic, hydrogen-bond networks to inter-connect extracellular and internal proton-binding sites, and to elicit conformational changes at the cytoplasmic G-protein binding site.
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Affiliation(s)
- Bhav Kapur
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
- Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | | | - Michalis Lazaratos
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Herbert Nar
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Gisela Schnapp
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alejandro Giorgetti
- University of Verona, Department of Biotechnology, 37134 Verona, Italy
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania
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Henderson SW, Nourmohammadi S, Ramesh SA, Yool AJ. Aquaporin ion conductance properties defined by membrane environment, protein structure, and cell physiology. Biophys Rev 2022; 14:181-198. [PMID: 35340612 PMCID: PMC8921385 DOI: 10.1007/s12551-021-00925-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023] Open
Abstract
Aquaporins (AQPs) are multifunctional transmembrane channel proteins permeable to water and an expanding array of solutes. AQP-mediated ion channel activity was first observed when purified AQP0 from bovine lens was incorporated into lipid bilayers. Electrophysiological properties of ion-conducting AQPs since discovered in plants, invertebrates, and mammals have been assessed using native, reconstituted, and heterologously expressed channels. Accumulating evidence is defining amino acid residues that govern differential solute permeability through intrasubunit and central pores of AQP tetramers. Rings of charged and hydrophobic residues around pores influence AQP selectivity, and are candidates for further work to define motifs that distinguish ion conduction capability, versus strict water and glycerol permeability. Similarities between AQP ion channels thus far include large single channel conductances and long open times, but differences in ionic selectivity, permeability to divalent cations, and mechanisms of gating (e.g., by voltage, pH, and cyclic nucleotides) are unique to subtypes. Effects of lipid environments in modulating parameters such as single channel amplitude could explain in part the variations in AQP ion channel properties observed across preparations. Physiological roles of the ion-conducting AQP classes span diverse processes including regulation of cell motility, organellar pH, neural development, signaling, and nutrient acquisition. Advances in computational methods can generate testable predictions of AQP structure-function relationships, which combined with innovative high-throughput assays could revolutionize the field in defining essential properties of ion-conducting AQPs, discovering new AQP ion channels, and understanding the effects of AQP interactions with proteins, signaling cascades, and membrane lipids.
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Affiliation(s)
- Sam W. Henderson
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005 Australia
| | | | - Sunita A. Ramesh
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042 Australia
| | - Andrea J. Yool
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005 Australia
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Herrera-Cazares LA, Luzardo-Ocampo I, Ramírez-Jiménez AK, Gutiérrez-Uribe JA, Campos-Vega R, Gaytán-Martínez M. Influence of extrusion process on the release of phenolic compounds from mango (Mangifera indica L.) bagasse-added confections and evaluation of their bioaccessibility, intestinal permeability, and antioxidant capacity. Food Res Int 2021; 148:110591. [PMID: 34507736 DOI: 10.1016/j.foodres.2021.110591] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022]
Abstract
Extruded polyphenol-rich by-products like mango bagasse (MB) could be used to manufacture functional confections. However, few reports have assessed the extrusion impact on MB polyphenols within a food matrix. This research aimed to evaluate the impact of extrusion on the bioaccessibility, intestinal permeability, and antioxidant capacity of phenolic compounds (PC) from non-extruded and extruded MB-added confections (EMBC and MBC, respectively). The inhibition of 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 2,2-diphenyl-1-picrylhydrazyl radicals and in silico approaches were used to evaluate the antioxidant capacity. MBC displayed the highest gastric bioaccessibility (%) of xanthones and flavonoids, whereas selective release of gallic acid, mangiferin, and quercetin glucoside was shown for EMBC. Lower PC' apparent permeability coefficients were found in EMBC compared to MB (0.11 to 0.44-fold change, p < 0.05). EMBC displayed the highest antioxidant capacity by the DPPH method for the non-digestible fraction, being mangiferin the highest in silico contributor (-4 kcal/mol). Our results showed that the extrusion process helps release selective phenolics from MBC, which increases their bioaccessibility and intestinal permeability.
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Affiliation(s)
- Luz Abril Herrera-Cazares
- Research and Graduate Studies in Food Science, School of Chemistry, Universidad Autónoma de Querétaro, Centro Universitario, Cerro de las Campanas S/N, Santiago de Querétaro, Querétaro 76010, Mexico
| | - Ivan Luzardo-Ocampo
- Research and Graduate Studies in Food Science, School of Chemistry, Universidad Autónoma de Querétaro, Centro Universitario, Cerro de las Campanas S/N, Santiago de Querétaro, Querétaro 76010, Mexico
| | - Aurea K Ramírez-Jiménez
- Tecnologico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, N.L., Mexico
| | - Janet A Gutiérrez-Uribe
- Tecnologico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, N.L., Mexico
| | - Rocio Campos-Vega
- Research and Graduate Studies in Food Science, School of Chemistry, Universidad Autónoma de Querétaro, Centro Universitario, Cerro de las Campanas S/N, Santiago de Querétaro, Querétaro 76010, Mexico
| | - Marcela Gaytán-Martínez
- Research and Graduate Studies in Food Science, School of Chemistry, Universidad Autónoma de Querétaro, Centro Universitario, Cerro de las Campanas S/N, Santiago de Querétaro, Querétaro 76010, Mexico.
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Abstract
This paper is the forty-second consecutive installment of the annual anthological review of research concerning the endogenous opioid system, summarizing articles published during 2019 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides and receptors as well as effects of opioid/opiate agonists and antagonists. The review is subdivided into the following specific topics: molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors (1), the roles of these opioid peptides and receptors in pain and analgesia in animals (2) and humans (3), opioid-sensitive and opioid-insensitive effects of nonopioid analgesics (4), opioid peptide and receptor involvement in tolerance and dependence (5), stress and social status (6), learning and memory (7), eating and drinking (8), drug abuse and alcohol (9), sexual activity and hormones, pregnancy, development and endocrinology (10), mental illness and mood (11), seizures and neurologic disorders (12), electrical-related activity and neurophysiology (13), general activity and locomotion (14), gastrointestinal, renal and hepatic functions (15), cardiovascular responses (16), respiration and thermoregulation (17), and immunological responses (18).
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and Neuropsychology Doctoral Sub-Program, Queens College, City University of New York, 65-30 Kissena Blvd., Flushing, NY, 11367, United States.
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