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Chen X, Yuan Y, Chen Y, Yu J, Wang J, Chen J, Guo Y, Pu X. Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from μOR/δOR Dimers. J Chem Inf Model 2022; 62:5581-5600. [PMID: 36377848 DOI: 10.1021/acs.jcim.2c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
GPCRs regulate multiple intracellular signaling cascades. Biasedly activating one signaling pathway over the others provides additional clinical utility to optimize GPCR-based therapies. GPCR heterodimers possess different functions from their monomeric states, including their selectivity to different transducers. However, the biased signaling mechanism induced by the heterodimerization remains unclear. Motivated by the issue, we select an important GPCR heterodimer (μOR/δOR heterodimer) as a case and use microsecond Gaussian accelerated molecular dynamics simulation coupled with potential of mean force and protein structure network (PSN) to probe mechanisms regarding the heterodimerization-induced constitutive β-arrestin activity and efficacy change of the agonist DAMGO. The results show that only the lowest energy state of the μOR/δOR heterodimer, which adopts a slightly outward shift of TM6 and an ICL2 conformation close to the receptor core, can selectively accommodate β-arrestins. PSN further reveals important roles of H8, ICL1, and ICL2 in regulating the constitutive β-arrestin-biased activity for the apo μOR/δOR heterodimer. In addition, the heterodimerization can allosterically alter the binding mode of DAMGO mainly by means of W7.35. Consequently, DAMGO transmits the structural signal mainly through TM6 and TM7 in the dimer, rather than TM3 similar to the μOR monomer, thus changing the efficacy of DAMGO from a balanced agonist to the β-arrestin-biased one. On the other side, the binding of DAMGO to the heterodimer can stabilize μOR/δOR heterodimers through a stronger interaction of TM1/TM1 and H8/H8, accordingly enhancing the interaction of μOR with δOR and the binding affinity of the dimer to the β-arrestin. The agonist DAMGO does not change main compositions of the regulation network from the dimer interface to the transducer binding pocket of the μOR protomer, but induces an increase in the structural communication of the network, which should contribute to the enhanced β-arrestin coupling. Our observations, for the first time, reveal the molecular mechanism of the biased signaling induced by the heterodimerization for GPCRs, which should be beneficial to more comprehensively understand the GPCR bias signaling.
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Affiliation(s)
- Xin Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu610041, China
| | - Yichi Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, California92697, United States
| | - Jingzhou Wang
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu610064, China
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Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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Park PSH. Supramolecular organization of rhodopsin in rod photoreceptor cell membranes. Pflugers Arch 2021; 473:1361-1376. [PMID: 33591421 DOI: 10.1007/s00424-021-02522-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 11/30/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells that initiates scotopic vision. Studies on the light receptor span well over a century, yet questions about the organization of rhodopsin within the photoreceptor cell membrane still persist and a consensus view on the topic is still elusive. Rhodopsin has been intensely studied for quite some time, and there is a wealth of information to draw from to formulate an organizational picture of the receptor in native membranes. Early experimental evidence in apparent support for a monomeric arrangement of rhodopsin in rod photoreceptor cell membranes is contrasted and reconciled with more recent visual evidence in support of a supramolecular organization of rhodopsin. What is known so far about the determinants of forming a supramolecular structure and possible functional roles for such an organization are also discussed. Many details are still missing on the structural and functional properties of the supramolecular organization of rhodopsin in rod photoreceptor cell membranes. The emerging picture presented here can serve as a springboard towards a more in-depth understanding of the topic.
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Affiliation(s)
- Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding. J Chem Theory Comput 2020; 16:1834-1842. [PMID: 31972074 DOI: 10.1021/acs.jctc.9b01035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Energetic contributions at the single-residue level for retinal-opsin interactions in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but antisymmetric to some extent. Fourteen residues were identified to be major players in retinal relaxation along a plausible pathway from bathorhodopsin to the blue-shifted intermediate, which is in good agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.
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Affiliation(s)
- Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Lei T, Hu Z, Ding R, Chen J, Li S, Zhang F, Pu X, Zhao N. Exploring the Activation Mechanism of a Metabotropic Glutamate Receptor Homodimer via Molecular Dynamics Simulation. ACS Chem Neurosci 2020; 11:133-145. [PMID: 31815422 DOI: 10.1021/acschemneuro.9b00425] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Metabotropic glutamate receptors of class C GPCRs exist as constitutive dimers, which play important roles in activating excitatory synapses of the central nervous system. However, the activation mechanism induced by agonists has not been clarified in experiments. To address the problem, we used microsecond all-atom molecular dynamics (MD) simulation couple with protein structure network (PSN) to explore the glutamate-induced activation for the mGluR1 homodimer. The results indicate that glutamate binding stabilizes not only the closure of Venus flytrap domains but also the polar interaction of LB2-LB2, in turn keeping the extracelluar domain in the active state. The activation of the extracelluar domain drives transmembrane domains (TMDs) of the two protomers closer and induces asymmetric activation for the TMD domains of the two protomers. One protomer with lower binding affinity to the agonist is activated, while the other protomer with higher binding energy is still in the inactive state. The PSN analysis identifies the allosteric regulation pathway from the ligand-binding pocket in the extracellular domain to the G-protein binding site in the intracellular TMD region and further reveals that the asymmetric activation is attributed to a combination of trans-pathway and cis-pathway regulations from two glumatates, rather than a single activation pathway. These observations could provide valuable molecular information for understanding of the structure and the implications in drug efficacy for the class C GPCR dimers.
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Affiliation(s)
- Ting Lei
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Zhenxin Hu
- College of Computer Science, Sichuan University, Chengdu 610064, China
| | - Ruolin Ding
- West China School of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shiqi Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Fuhui Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
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Barreto CAV, Baptista SJ, Preto AJ, Matos-Filipe P, Mourão J, Melo R, Moreira I. Prediction and targeting of GPCR oligomer interfaces. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:105-149. [PMID: 31952684 DOI: 10.1016/bs.pmbts.2019.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
GPCR oligomerization has emerged as a hot topic in the GPCR field in the last years. Receptors that are part of these oligomers can influence each other's function, although it is not yet entirely understood how these interactions work. The existence of such a highly complex network of interactions between GPCRs generates the possibility of alternative targets for new therapeutic approaches. However, challenges still exist in the characterization of these complexes, especially at the interface level. Different experimental approaches, such as FRET or BRET, are usually combined to study GPCR oligomer interactions. Computational methods have been applied as a useful tool for retrieving information from GPCR sequences and the few X-ray-resolved oligomeric structures that are accessible, as well as for predicting new and trustworthy GPCR oligomeric interfaces. Machine-learning (ML) approaches have recently helped with some hindrances of other methods. By joining and evaluating multiple structure-, sequence- and co-evolution-based features on the same algorithm, it is possible to dilute the issues of particular structures and residues that arise from the experimental methodology into all-encompassing algorithms capable of accurately predict GPCR-GPCR interfaces. All these methods used as a single or a combined approach provide useful information about GPCR oligomerization and its role in GPCR function and dynamics. Altogether, we present experimental, computational and machine-learning methods used to study oligomers interfaces, as well as strategies that have been used to target these dynamic complexes.
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Affiliation(s)
- Carlos A V Barreto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Salete J Baptista
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, CTN, LRS, Portugal
| | - António José Preto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Pedro Matos-Filipe
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Rita Melo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, CTN, LRS, Portugal
| | - Irina Moreira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Science and Technology Faculty, University of Coimbra, Coimbra, Portugal.
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Li Y, Wang M, Gao N, Li D, Lin J. The effect of dimerization on the activation and conformational dynamics of adenosine A 1 receptor. Phys Chem Chem Phys 2019; 21:22763-22773. [PMID: 31595279 DOI: 10.1039/c9cp04060a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adenosine A1 receptor (A1R) is one of four adenosine receptors in humans, which are involved in the function of the cardiovascular, respiratory and central nervous systems. Experimental results indicate that A1R can form a homodimer and that the protomer-protomer interaction in the A1R dimer is related to certain pharmacological characteristics of A1R activation. In this work, we performed docking, metadynamics simulation, conventional molecular dynamics simulations, Gaussian-accelerated molecular dynamics simulations, potential of mean force calculations, dynamic cross-correlation motions analysis and community network analysis to study the binding mode of 5'-N-ethylcarboxamidoadenosine (NECA) to A1R and the effect of dimerization on the activation of A1R. Our results show that NECA binds to A1R in a similar mode to adenosine in the A1R crystal structure and NECA in the A2AR crystal structure. The A1R homodimer can be activated by one or two agonists with NECA occupying its orthosteric pockets in one (which we call the NECA-A1R system) or both protomers (which we call the dNECA-A1R system). In the NECA-A1R system, activation is predicated in the protomer without NECA bound. In the dNECA-A1R system, only one protomer achieves the active state. These findings suggest an asymmetrical activation mechanism of the homodimer and a negative cooperativity between the two protomers. We envision that our results may further facilitate the drug development of A1R.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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8
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Zhang X, Yuan Y, Wang L, Guo Y, Li M, Li C, Pu X. Use multiscale simulation to explore the effects of the homodimerizations between different conformation states on the activation and allosteric pathway for the μ-opioid receptor. Phys Chem Chem Phys 2018; 20:13485-13496. [PMID: 29726867 DOI: 10.1039/c8cp02016g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recently, oligomers of G-protein coupled receptors (GPCRs) have been an important topic in the GPCR fields. However, knowledge about their structures and activation mechanisms is very limited due to the absence of crystal structures reported. In this work, we used multiscale simulations to study the effects of homodimerization between different conformation states on their activation, dynamic behaviors, and allosteric communication pathways for μ-OR. The results indicated that the dimerization of one inactive monomer with either one inactive monomer or one active one could enhance its constitutive activation. However, the conformation state of the other protomer (e.g., active or inactive) can influence the activated extent. The dimerization between the two inactive protomers leads to a negative cooperativity for their activation, which should contribute to the asymmetric activation of GPCR dimers observed in some experiments. On the other hand, for the active monomer, its dimerization with one inactive receptor could alleviate its deactivation, whereby negative and positive cooperativities can be observed between the two subunits of the dimer, depending on the different regions. Observations from protein structure network (PSN) analysis indicated that the dimerization of one inactive monomer with one active one would cause a significant drop in the number of main pathways from the ligand binding pocket to the G-protein coupled region for the inactive protomer, while the impact is minor for the active protomer. But, for the active monomer or the inactive one, its dimerization with one inactive monomer would significantly change the types of residues participating in the pathway with the highest frequency.
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Affiliation(s)
- Xi Zhang
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, P. R. China
| | - Longrong Wang
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, Sichuan 610064, P. R. China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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9
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Apo-Opsin Exists in Equilibrium Between a Predominant Inactive and a Rare Highly Active State. J Neurosci 2018; 39:212-223. [PMID: 30459230 DOI: 10.1523/jneurosci.1980-18.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 12/17/2022] Open
Abstract
Bleaching adaptation in rod photoreceptors is mediated by apo-opsin, which activates phototransduction with effective activity 105- to 106-fold lower than that of photoactivated rhodopsin (meta II). However, the mechanism that produces such low opsin activity is unknown. To address this question, we sought to record single opsin responses in mouse rods. We used mutant mice lacking efficient calcium feedback to boosts rod responses and generated a small fraction of opsin by photobleaching ∼1% of rhodopsin. The bleach produced a dramatic increase in the frequency of discrete photoresponse-like events. This activity persisted for hours, was quenched by 11-cis-retinal, and was blocked by uncoupling opsin from phototransduction, all indicating opsin as its source. Opsin-driven discrete activity was also observed in rods containing non-activatable rhodopsin, ruling out transactivation of rhodopsin by opsin. We conclude that bleaching adaptation is mediated by opsin that exists in equilibrium between a predominant inactive and a rare meta II-like state.SIGNIFICANCE STATEMENT Electrophysiological analysis is used to show that the G-protein-coupled receptor opsin exists in equilibrium between a predominant inactive and a rare highly active state that mediates bleaching adaptation in photoreceptors.
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Detection of misfolded rhodopsin aggregates in cells by Förster resonance energy transfer. Methods Cell Biol 2018; 149:87-105. [PMID: 30616829 DOI: 10.1016/bs.mcb.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells of the retina that plays a central role in phototransduction and rod photoreceptor cell health. Rhodopsin mutations are the leading known cause of autosomal dominant retinitis pigmentosa, a retinal degenerative disease. A majority of rhodopsin mutations cause misfolding and aggregation of the apoprotein opsin. The nature of aggregates formed by misfolded rhodopsin mutants and the associated cell toxicity is poorly understood. Misfolding rhodopsin mutants have been characterized biochemically, and categorized as either partial or complete misfolding mutants. This classification is incomplete and does not provide sufficient information to fully understand rhodopsin aggregation, disease pathogenesis, and evaluate therapeutic strategies. To better understand the aggregation of misfolded rhodopsin mutants, a Förster resonance energy transfer assay has been developed to monitor the aggregation of fluorescently tagged mutant rhodopsins expressed in live cells.
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11
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Gragg M, Park PSH. Misfolded rhodopsin mutants display variable aggregation properties. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2938-2948. [PMID: 29890221 PMCID: PMC6066411 DOI: 10.1016/j.bbadis.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 11/20/2022]
Abstract
The largest class of rhodopsin mutations causing autosomal dominant retinitis pigmentosa (adRP) is mutations that lead to misfolding and aggregation of the receptor. The misfolding mutants have been characterized biochemically, and categorized as either partial or complete misfolding mutants. This classification is incomplete and does not provide sufficient information to fully understand the disease pathogenesis and evaluate therapeutic strategies. A Förster resonance energy transfer (FRET) method was utilized to directly assess the aggregation properties of misfolding rhodopsin mutants within the cell. Partial (P23H and P267L) and complete (G188R, H211P, and P267R) misfolding mutants were characterized to reveal variability in aggregation properties. The complete misfolding mutants all behaved similarly, forming aggregates when expressed alone, minimally interacting with the wild-type receptor when coexpressed, and were unresponsive to treatment with the pharmacological chaperone 9-cis retinal. In contrast, variability was observed between the partial misfolding mutants. In the opsin form, the P23H mutant behaved similarly as the complete misfolding mutants. In contrast, the opsin form of the P267L mutant existed as both aggregates and oligomers when expressed alone and formed mostly oligomers with the wild-type receptor when coexpressed. The partial misfolding mutants both reacted similarly to the pharmacological chaperone 9-cis retinal, displaying improved folding and oligomerization when expressed alone but aggregating with wild-type receptor when coexpressed. The observed differences in aggregation properties and effect of 9-cis retinal predict different outcomes in disease pathophysiology and suggest that retinoid-based chaperones will be ineffective or even detrimental.
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Affiliation(s)
- Megan Gragg
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
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12
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Durdagi S, Erol I, Salmas RE, Aksoydan B, Kantarcioglu I. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors. Neurosci Lett 2018; 700:30-37. [PMID: 29684528 DOI: 10.1016/j.neulet.2018.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022]
Abstract
G Protein-Coupled Receptors (GPCRs) can form homo- and heterodimers or constitute higher oligomeric clusters with other heptahelical GPCRs. In this article, multiscale molecular modeling approaches as well as experimental techniques which are used to study oligomerization of GPCRs are reviewed. In particular, the effect of dimerization/oligomerization to the ligand binding affinity of individual protomers and also on the efficacy of the oligomer are discussed by including diverse examples from the literature. In addition, possible allosteric effects that may emerge upon interaction of GPCRs with membrane components, like cholesterol, is also discussed. Investigation of these above-mentioned interactions may greatly contribute to the candidate molecule screening studies and development of novel therapeutics with fewer adverse effects.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
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Wang L, Yuan Y, Chen X, Chen J, Guo Y, Li M, Li C, Pu X. Probing the cooperative mechanism of the μ–δ opioid receptor heterodimer by multiscale simulation. Phys Chem Chem Phys 2018; 20:29969-29982. [DOI: 10.1039/c8cp06652c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The activation-cooperativity of the μ–δ opioid receptor heterodimer was probed by multiscale simulation coupled with a protein structure network.
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Affiliation(s)
- Longrong Wang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610041
- P. R. China
| | - Xin Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Jiangfan Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Chuan Li
- College of Computer Science
- Sichuan University
- Chengdu
- P. R. China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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15
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Altwaijry NA, Baron M, Wright DW, Coveney PV, Townsend-Nicholson A. An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2017; 13:2254-2270. [PMID: 28383913 PMCID: PMC5557214 DOI: 10.1021/acs.jctc.6b01246] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
The
accurate identification of the specific points of interaction
between G protein-coupled receptor (GPCR) oligomers is essential for
the design of receptor ligands targeting oligomeric receptor targets.
A coarse-grained molecular dynamics computer simulation approach would
provide a compelling means of identifying these specific protein–protein
interactions and could be applied both for known oligomers of interest
and as a high-throughput screen to identify novel oligomeric targets.
However, to be effective, this in silico modeling must provide accurate,
precise, and reproducible information. This has been achieved recently
in numerous biological systems using an ensemble-based all-atom molecular
dynamics approach. In this study, we describe an equivalent methodology
for ensemble-based coarse-grained simulations. We report the performance
of this method when applied to four different GPCRs known to oligomerize
using error analysis to determine the ensemble size and individual
replica simulation time required. Our measurements of distance between
residues shown to be involved in oligomerization of the fifth transmembrane
domain from the adenosine A2A receptor are in very good
agreement with the existing biophysical data and provide information
about the nature of the contact interface that cannot be determined
experimentally. Calculations of distance between rhodopsin, CXCR4,
and β1AR transmembrane domains reported to form contact
points in homodimers correlate well with the corresponding measurements
obtained from experimental structural data, providing an ability to predict
contact interfaces computationally. Interestingly, error analysis
enables identification of noninteracting regions. Our results confirm
that GPCR interactions can be reliably predicted using this novel
methodology.
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Affiliation(s)
- Nojood A Altwaijry
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, United Kingdom.,King Saud University , Riyadh, Kingdom of Saudi Arabia
| | - Michael Baron
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, United Kingdom
| | - David W Wright
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Andrea Townsend-Nicholson
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London , London, WC1E 6BT, United Kingdom
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16
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Kamiya M, Hayashi S. Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation. J Phys Chem B 2017; 121:3842-3852. [PMID: 28240904 DOI: 10.1021/acs.jpcb.6b13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.
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Affiliation(s)
- Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
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17
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Methods used to study the oligomeric structure of G-protein-coupled receptors. Biosci Rep 2017; 37:BSR20160547. [PMID: 28062602 PMCID: PMC5398257 DOI: 10.1042/bsr20160547] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 02/02/2023] Open
Abstract
G-protein-coupled receptors (GPCRs), which constitute the largest family of cell surface receptors, were originally thought to function as monomers, but are now recognized as being able to act in a wide range of oligomeric states and indeed, it is known that the oligomerization state of a GPCR can modulate its pharmacology and function. A number of experimental techniques have been devised to study GPCR oligomerization including those based upon traditional biochemistry such as blue-native PAGE (BN-PAGE), co-immunoprecipitation (Co-IP) and protein-fragment complementation assays (PCAs), those based upon resonance energy transfer, FRET, time-resolved FRET (TR-FRET), FRET spectrometry and bioluminescence resonance energy transfer (BRET). Those based upon microscopy such as FRAP, total internal reflection fluorescence microscopy (TIRFM), spatial intensity distribution analysis (SpIDA) and various single molecule imaging techniques. Finally with the solution of a growing number of crystal structures, X-ray crystallography must be acknowledged as an important source of discovery in this field. A different, but in many ways complementary approach to the use of more traditional experimental techniques, are those involving computational methods that possess obvious merit in the study of the dynamics of oligomer formation and function. Here, we summarize the latest developments that have been made in the methods used to study GPCR oligomerization and give an overview of their application.
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18
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Capra V, Mauri M, Guzzi F, Busnelli M, Accomazzo MR, Gaussem P, Nisar SP, Mundell SJ, Parenti M, Rovati GE. Impaired thromboxane receptor dimerization reduces signaling efficiency: A potential mechanism for reduced platelet function in vivo. Biochem Pharmacol 2016; 124:43-56. [PMID: 27845050 DOI: 10.1016/j.bcp.2016.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/10/2016] [Indexed: 12/16/2022]
Abstract
Thromboxane A2 is a potent mediator of inflammation and platelet aggregation exerting its effects through the activation of a G protein-coupled receptor (GPCR), termed TP. Although the existence of dimers/oligomers in Class A GPCRs is widely accepted, their functional significance still remains controversial. Recently, we have shown that TPα and TPβ homo-/hetero-dimers interact through an interface of residues in transmembrane domain 1 (TM1) whose disruption impairs dimer formation. Here, biochemical and pharmacological characterization of this dimer deficient mutant (DDM) in living cells indicates a significant impairment in its response to agonists. Interestingly, two single loss-of-function TPα variants, namely W29C and N42S recently identified in two heterozygous patients affected by bleeding disorders, match some of the residues mutated in our DDM. These two naturally occurring variants display a reduced potency to TP agonists and are characterized by impaired dimer formation in transfected HEK-293T cells. These findings provide proofs that lack of homo-dimer formation is a crucial process for reduced TPα function in vivo, and might represent one molecular mechanism through which platelet TPα receptor dysfunction affects the patient(s) carrying these mutations.
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Key Words
- (Z)-7-[(1R,2R,3R,4S)-3-[[2-(phenylcarbamoyl)hydrazinyl]methyl]-7-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid
- (Z)-7-[(1S,2S,3R,4R)-3-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid
- (Z)-7-[(1S,2S,3S,4R)-3-[(E,3R)-3-hydroxy-4-(4-iodophenoxy)but-1-enyl]-7-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid
- (Z)-7-[(1S,3R,4R,5S)-3-[(E,3R)-3-hydroxyoct-1-enyl]-6,6-dimethyl-4-bicyclo[3.1.1]heptanyl]hept-5-enoic acid
- 3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid
- Eicosanoids
- G protein coupled receptors
- I-BOP (PubChem CID: 51015454)
- Pinane Thromboxane A2 (PTA2) (PubChem CID: 25834471)
- Platelets
- Ramatroban (PubChem CID: 123879)
- Receptor dimer
- SQ29,548 (PubChem CID: 6437074)
- Signal transduction
- Thromboxane A(2)
- U46619 (PubChem CID: 5311493)
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Affiliation(s)
- Valérie Capra
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy; Department of Health Science, University of Milan, Milano, Italy.
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - Francesca Guzzi
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - Marta Busnelli
- CNR, Institute of Neuroscience, University of Milan, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy.
| | - Maria Rosa Accomazzo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
| | - Pascale Gaussem
- Inserm UMR-S1140, Faculte' de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité, Paris and AP-HP, Hopital Européen Georges Pompidou, Service d'Hématologie Biologique, Paris, France.
| | - Shaista P Nisar
- School of Physiology and Pharmacology, University of Bristol, Bristol BS8 1TD, UK.
| | - Stuart J Mundell
- School of Physiology and Pharmacology, University of Bristol, Bristol BS8 1TD, UK.
| | - Marco Parenti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
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19
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Morrow JM, Lazic S, Dixon Fox M, Kuo C, Schott RK, de A Gutierrez E, Santini F, Tropepe V, Chang BSW. A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes. ACTA ACUST UNITED AC 2016; 220:294-303. [PMID: 27811293 DOI: 10.1242/jeb.145953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022]
Abstract
Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1 We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1 These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.
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Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Savo Lazic
- Department of Molecular Genetics, University of Toronto, Toronto, Canada, M5S 1A8
| | - Monica Dixon Fox
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Claire Kuo
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Francesco Santini
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada, M5T 3A9.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5 .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
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20
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Jiang Y, Yuan Y, Zhang X, Liang T, Guo Y, Li M, Pu X. Use of network model to explore dynamic and allosteric properties of three GPCR homodimers. RSC Adv 2016. [DOI: 10.1039/c6ra18243g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We used an elastic network model and protein structure network to study three class A GPCR homodimers.
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Affiliation(s)
- Yuanyuan Jiang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610064
- P. R. China
| | - Xi Zhang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Tao Liang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yanzhi Guo
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Menglong Li
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Xumei Pu
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
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21
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Meng XY, Mezei M, Cui M. Computational approaches for modeling GPCR dimerization. Curr Pharm Biotechnol 2015; 15:996-1006. [PMID: 25307013 DOI: 10.2174/1389201015666141013102515] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/09/2014] [Accepted: 08/18/2014] [Indexed: 11/22/2022]
Abstract
Growing experimental evidences suggest that dimerization and oligomerization are important for G Protein- Coupled Receptors (GPCRs) function. The detailed structural information of dimeric/oligomeric GPCRs would be very important to understand their function. Although it is encouraging that recently several experimental GPCR structures in oligomeric forms have appeared, experimental determination of GPCR structures in oligomeric forms is still a big challenge, especially in mimicking the membrane environment. Therefore, development of computational approaches to predict dimerization of GPCRs will be highly valuable. In this review, we summarize computational approaches that have been developed and used for modeling of GPCR dimerization. In addition, we introduce a novel two-dimensional Brownian Dynamics based protein docking approach, which we have recently adapted, for GPCR dimer prediction.
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Affiliation(s)
| | | | - Meng Cui
- Institute of Quantitative Biology and Medicine, Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China.
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22
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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23
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Human infrared vision is triggered by two-photon chromophore isomerization. Proc Natl Acad Sci U S A 2014; 111:E5445-54. [PMID: 25453064 DOI: 10.1073/pnas.1410162111] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Vision relies on photoactivation of visual pigments in rod and cone photoreceptor cells of the retina. The human eye structure and the absorption spectra of pigments limit our visual perception of light. Our visual perception is most responsive to stimulating light in the 400- to 720-nm (visible) range. First, we demonstrate by psychophysical experiments that humans can perceive infrared laser emission as visible light. Moreover, we show that mammalian photoreceptors can be directly activated by near infrared light with a sensitivity that paradoxically increases at wavelengths above 900 nm, and display quadratic dependence on laser power, indicating a nonlinear optical process. Biochemical experiments with rhodopsin, cone visual pigments, and a chromophore model compound 11-cis-retinyl-propylamine Schiff base demonstrate the direct isomerization of visual chromophore by a two-photon chromophore isomerization. Indeed, quantum mechanics modeling indicates the feasibility of this mechanism. Together, these findings clearly show that human visual perception of near infrared light occurs by two-photon isomerization of visual pigments.
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24
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Riahi S, Rowley CN. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties. J Comput Chem 2014; 35:2076-86. [PMID: 25178266 DOI: 10.1002/jcc.23716] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 01/05/2023]
Abstract
The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.
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Affiliation(s)
- Saleh Riahi
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3X7, Canada
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25
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Campomanes P, Neri M, Horta BAC, Röhrig UF, Vanni S, Tavernelli I, Rothlisberger U. Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle. J Am Chem Soc 2014; 136:3842-51. [DOI: 10.1021/ja411303v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Marilisa Neri
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Bruno A. C. Horta
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Molecular Modeling
Group, Swiss Institute of
Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefano Vanni
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
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26
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Doemer M, Maurer P, Campomanes P, Tavernelli I, Rothlisberger U. Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin. J Chem Theory Comput 2013; 10:412-22. [PMID: 26579920 DOI: 10.1021/ct400697n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.
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Affiliation(s)
- Manuel Doemer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Patrick Maurer
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Pablo Campomanes
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ivano Tavernelli
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
| | - Ursula Rothlisberger
- Laboratoire de Chimie et Biochimie Computationelle, Ecole Polytechnique Fédérale de Lausanne , Lausanne, CH-1025, Switzerland
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27
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Redka DS, Heerklotz H, Wells JW. Efficacy as an Intrinsic Property of the M2 Muscarinic Receptor in Its Tetrameric State. Biochemistry 2013; 52:7405-27. [DOI: 10.1021/bi4003869] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Dar’ya S. Redka
- Department of Pharmaceutical
Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada M5S 3M2
| | - Heiko Heerklotz
- Department of Pharmaceutical
Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada M5S 3M2
| | - James W. Wells
- Department of Pharmaceutical
Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada M5S 3M2
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28
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Jastrzebska B. GPCR: G protein complexes--the fundamental signaling assembly. Amino Acids 2013; 45:1303-14. [PMID: 24052187 DOI: 10.1007/s00726-013-1593-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 09/10/2013] [Indexed: 12/15/2022]
Abstract
G protein coupled receptors (GPCR) constitute the largest group of cell surface receptors that transmit various signals across biological membranes through the binding and activation of heterotrimeric G proteins, which amplify the signal and activate downstream effectors leading to the biological responses. Thus, the first critical step in this signaling cascade is the interaction between receptor and its cognate G protein. Understanding this critical event at the molecular level is of high importance because abnormal function of GPCRs is associated with many diseases. Thus, these receptors are targets for drug development.
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Affiliation(s)
- Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106-4965, USA,
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29
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Zhu S, Brown MF, Feller SE. Retinal conformation governs pKa of protonated Schiff base in rhodopsin activation. J Am Chem Soc 2013; 135:9391-8. [PMID: 23701524 PMCID: PMC5176254 DOI: 10.1021/ja4002986] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have explored the relationship between conformational energetics and the protonation state of the Schiff base in retinal, the covalently bound ligand responsible for activating the G protein-coupled receptor rhodopsin, using quantum chemical calculations. Guided by experimental structural determinations and large-scale molecular simulations on this system, we examined rotation about each bond in the retinal polyene chain, for both the protonated and deprotonated states that represent the dark and photoactivated states, respectively. Particular attention was paid to the torsional degrees of freedom that determine the shape of the molecule, and hence its interactions with the protein binding pocket. While most torsional degrees of freedom in retinal are characterized by large energetic barriers that minimize structural fluctuations under physiological temperatures, the C6-C7 dihedral defining the relative orientation of the β-ionone ring to the polyene chain has both modest barrier heights and a torsional energy surface that changes dramatically with protonation of the Schiff base. This surprising coupling between conformational degrees of freedom and protonation state is further quantified by calculations of the pKa as a function of the C6-C7 dihedral angle. Notably, pKa shifts of greater than two units arise from torsional fluctuations observed in molecular dynamics simulations of the full ligand-protein-membrane system. It follows that fluctuations in the protonation state of the Schiff base occur prior to forming the activated MII state. These new results shed light on important mechanistic aspects of retinal conformational changes that are involved in the activation of rhodopsin in the visual process.
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Affiliation(s)
- Shengshuang Zhu
- Department of Chemistry, Wabash College, Crawfordsville IN 47933
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson AZ 85721
- Department of Physics, University of Arizona, Tucson AZ 85721
| | - Scott E. Feller
- Department of Chemistry, Wabash College, Crawfordsville IN 47933
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Cascella M, Bärfuss S, Stocker A. Cis-retinoids and the chemistry of vision. Arch Biochem Biophys 2013; 539:187-95. [PMID: 23791723 DOI: 10.1016/j.abb.2013.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/04/2013] [Accepted: 06/10/2013] [Indexed: 11/17/2022]
Abstract
We discuss here principal biochemical transformations of retinoid molecules in the visual cycle. We focus our analysis on the accumulating evidence of alternate pathways and functional redundancies in the cycle. The efficiency of the visual cycle depends, on one hand, on fast regeneration of the photo-bleached chromophores. On the other hand, it is crucial that the cyclic process should be highly selective to avoid accumulation of byproducts. The state-of-the-art knowledge indicates that single enzymatically active components of the cycle are not strictly selective and may require chaperones to enhance their rates. It appears that protein-protein interactions significantly improve the biological stability of the visual cycle. In particular, synthesis of thermodynamically less stable 11-cis-retinoid conformers is favored by physical interactions of the isomerases present in the retina with cellular retinaldehyde binding protein.
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Affiliation(s)
- Michele Cascella
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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31
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Palczewski K, Orban T. From atomic structures to neuronal functions of g protein-coupled receptors. Annu Rev Neurosci 2013; 36:139-64. [PMID: 23682660 DOI: 10.1146/annurev-neuro-062012-170313] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
G protein-coupled receptors (GPCRs) are essential mediators of signal transduction, neurotransmission, ion channel regulation, and other cellular events. GPCRs are activated by diverse stimuli, including light, enzymatic processing of their N-termini, and binding of proteins, peptides, or small molecules such as neurotransmitters. GPCR dysfunction caused by receptor mutations and environmental challenges contributes to many neurological diseases. Moreover, modern genetic technology has helped identify a rich array of mono- and multigenic defects in humans and animal models that connect such receptor dysfunction with disease affecting neuronal function. The visual system is especially suited to investigate GPCR structure and function because advanced imaging techniques permit structural studies of photoreceptor neurons at both macro and molecular levels that, together with biochemical and physiological assessment in animal models, provide a more complete understanding of GPCR signaling.
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Affiliation(s)
- Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA.
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32
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Valsson O, Campomanes P, Tavernelli I, Rothlisberger U, Filippi C. Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls. J Chem Theory Comput 2013; 9:2441-54. [PMID: 26583734 DOI: 10.1021/ct3010408] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophore-protein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms.
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Affiliation(s)
- Omar Valsson
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
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33
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Palermo G, Campomanes P, Neri M, Piomelli D, Cavalli A, Rothlisberger U, De Vivo M. Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis. J Chem Theory Comput 2013; 9:1202-13. [PMID: 26588763 DOI: 10.1021/ct300611q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine hydrolase, fatty acid amide hydrolase (FAAH), is responsible for the intracellular degradation of anandamide and other bioactive fatty acid ethanolamides involved in the regulation of pain, inflammation, and other pathophysiological processes. The catalytic site of FAAH is composed of multiple cavities with mixed hydrophobic and hydrophilic properties, the role of which remains incompletely understood. Anandamide is thought to enter the active site through a "membrane-access" (MA) channel and position its flexible fatty acyl chain in a highly hydrophobic "acyl chain-binding" (AB) cavity to allow for hydrolysis to occur. Using microsecond molecular dynamics (MD) simulations of FAAH embedded in a realistic membrane/water environment, we show now that anandamide may not lock itself into the AB cavity but may rather assume catalytically significant conformations required for hydrolysis by moving its flexible arachidonoyl tail between the MA and AB cavities. This process is regulated by a phenylalanine residue (Phe432) located at the boundary between the two cavities, which may act as a "dynamic paddle." The results identify structural flexibility as a key determinant by which FAAH recognizes its primary lipid substrate.
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Affiliation(s)
- Giulia Palermo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.,Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marilisa Neri
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Daniele Piomelli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.,Department of Anatomy and Neurobiology, University of California, Irvine, California 92697, United States
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.,Department of Pharmaceutical Sciences, University of Bologna, via Belmeloro 6, I-40126 Bologna, Italy
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
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Jastrzebska B, Orban T, Golczak M, Engel A, Palczewski K. Asymmetry of the rhodopsin dimer in complex with transducin. FASEB J 2013; 27:1572-84. [PMID: 23303210 DOI: 10.1096/fj.12-225383] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A large body of evidence for G-protein-coupled receptor (GPCR) oligomerization has accumulated over the past 2 decades. The smallest of these oligomers in vivo most likely is a dimer that buries 1000-Å(2) intramolecular surfaces and on stimulation forms a complex with heterotrimeric G protein in 2:1 stoichiometry. However, it is unclear whether each of the monomers adopts the same or a different conformation and function after activation of this dimer. With bovine rhodopsin (Rho) and its cognate bovine G-protein transducin (Gt) as a model system, we used the retinoid chromophores 11-cis-retinal and 9-cis-retinal to monitor each monomer of the dimeric GPCR within a stable complex with nucleotide-free Gt. We found that only 50% of Rho* in the Rho*-Gt complex is trapped in a Meta II conformation, while 50% evolves toward an opsin conformation and can be regenerated with 9-cis-retinal. We also found that all-trans-retinal can regenerate chromophore-depleted Rho*e complexed with Gt and FAK*TSA peptide containing Lys(296) with the attached all-trans retinoid (m/z of 934.5[MH](+)) was identified by mass spectrometry. Thus, our study shows that each of the monomers contributes unequally to the pentameric (2:1:1:1) complex of Rho dimer and Gt heterotrimer, validating the oligomeric structure of the complex and the asymmetry of the GPCR dimer, and revealing its structural/functional signature. This study provides a clear functional distinction between monomers of family A GPCRs in their oligomeric form.
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Affiliation(s)
- Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA
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35
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Taddese B, Simpson LM, Wall ID, Blaney FE, Reynolds CA. Modeling Active GPCR Conformations. Methods Enzymol 2013; 522:21-35. [DOI: 10.1016/b978-0-12-407865-9.00002-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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36
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Trzaskowski B, Latek D, Yuan S, Ghoshdastider U, Debinski A, Filipek S. Action of molecular switches in GPCRs--theoretical and experimental studies. Curr Med Chem 2012; 19:1090-109. [PMID: 22300046 PMCID: PMC3343417 DOI: 10.2174/092986712799320556] [Citation(s) in RCA: 333] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/30/2011] [Accepted: 01/02/2012] [Indexed: 01/14/2023]
Abstract
G protein coupled receptors (GPCRs), also called 7TM receptors, form a huge superfamily of membrane proteins that, upon activation by extracellular agonists, pass the signal to the cell interior. Ligands can bind either to extracellular N-terminus and loops (e.g. glutamate receptors) or to the binding site within transmembrane helices (Rhodopsin-like family). They are all activated by agonists although a spontaneous auto-activation of an empty receptor can also be observed. Biochemical and crystallographic methods together with molecular dynamics simulations and other theoretical techniques provided models of the receptor activation based on the action of so-called "molecular switches" buried in the receptor structure. They are changed by agonists but also by inverse agonists evoking an ensemble of activation states leading toward different activation pathways. Switches discovered so far include the ionic lock switch, the 3-7 lock switch, the tyrosine toggle switch linked with the nPxxy motif in TM7, and the transmission switch. The latter one was proposed instead of the tryptophan rotamer toggle switch because no change of the rotamer was observed in structures of activated receptors. The global toggle switch suggested earlier consisting of a vertical rigid motion of TM6, seems also to be implausible based on the recent crystal structures of GPCRs with agonists. Theoretical and experimental methods (crystallography, NMR, specific spectroscopic methods like FRET/BRET but also single-molecule-force-spectroscopy) are currently used to study the effect of ligands on the receptor structure, location of stable structural segments/domains of GPCRs, and to answer the still open question on how ligands are binding: either via ensemble of conformational receptor states or rather via induced fit mechanisms. On the other hand the structural investigations of homoand heterodimers and higher oligomers revealed the mechanism of allosteric signal transmission and receptor activation that could lead to design highly effective and selective allosteric or ago-allosteric drugs.
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Affiliation(s)
- B Trzaskowski
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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37
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Mertz B, Struts AV, Feller SE, Brown MF. Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:241-51. [PMID: 21851809 PMCID: PMC5270601 DOI: 10.1016/j.bbamem.2011.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Revised: 08/01/2011] [Accepted: 08/01/2011] [Indexed: 10/17/2022]
Abstract
Rhodopsin has served as the primary model for studying G protein-coupled receptors (GPCRs)-the largest group in the human genome, and consequently a primary target for pharmaceutical development. Understanding the functions and activation mechanisms of GPCRs has proven to be extraordinarily difficult, as they are part of a complex signaling cascade and reside within the cell membrane. Although X-ray crystallography has recently solved several GPCR structures that may resemble the activated conformation, the dynamics and mechanism of rhodopsin activation continue to remain elusive. Notably solid-state ((2))H NMR spectroscopy provides key information pertinent to how local dynamics of the retinal ligand change during rhodopsin activation. When combined with molecular mechanics simulations of proteolipid membranes, a new paradigm for the rhodopsin activation process emerges. Experiment and simulation both suggest that retinal isomerization initiates the rhodopsin photocascade to yield not a single activated structure, but rather an ensemble of activated conformational states. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Blake Mertz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Andrey V. Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Medical Physics, St. Petersburg State Medical University, St. Petersburg 194100, Russia
| | - Scott E. Feller
- Department of Chemistry, Wabash College, Crawfordsville, IN 47933, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Physics, University of Arizona, Tucson, AZ 85721, USA
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38
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Bruno A, Costantino G. Molecular Dynamics Simulations of G Protein-Coupled Receptors. Mol Inform 2012; 31:222-30. [DOI: 10.1002/minf.201100138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/18/2011] [Indexed: 12/14/2022]
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39
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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40
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Johnston JM, Filizola M. Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors. Curr Opin Struct Biol 2011; 21:552-8. [PMID: 21764295 DOI: 10.1016/j.sbi.2011.06.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 06/06/2011] [Accepted: 06/21/2011] [Indexed: 12/30/2022]
Abstract
Despite many years of dedicated efforts, high-resolution structural determination of membrane proteins lags far behind that of soluble proteins. Computational methods in general, and molecular dynamics (MD) simulations in particular, have represented important alternative resources over the years to advance understanding of membrane protein structure and function. However, it is only recently that much progress has been achieved owing to new high-resolution membrane protein structures, specialized parallel computer architectures, and efficient simulation algorithms. This has definitely been the case for G protein-coupled receptors (GPCRs), which have assumed a leading role in the area of structural biology with several new structures appearing in the literature during the past five years. We provide here a concise overview of recent developments in computational biophysics of membrane proteins, using GPCRs as an example to showcase important information that can be derived from modern MD simulations.
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Affiliation(s)
- Jennifer M Johnston
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
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41
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McGeagh JD, Ranaghan KE, Mulholland AJ. Protein dynamics and enzyme catalysis: insights from simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1077-92. [PMID: 21167324 DOI: 10.1016/j.bbapap.2010.12.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/25/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- John D McGeagh
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, BS8 1TS, United Kingdom
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42
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Monnier C, Tu H, Bourrier E, Vol C, Lamarque L, Trinquet E, Pin JP, Rondard P. Trans-activation between 7TM domains: implication in heterodimeric GABAB receptor activation. EMBO J 2010; 30:32-42. [PMID: 21063387 DOI: 10.1038/emboj.2010.270] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/06/2010] [Indexed: 02/06/2023] Open
Abstract
Seven-transmembrane domain (7TM) receptors have important functions in cell-cell communication and can assemble into dimers or oligomers. Such complexes may allow specific functional cross-talk through trans-activation of interacting 7TMs, but this hypothesis requires further validation. Herein, we used the GABAB receptor, which is composed of two distinct subunits, GABAB1, which binds the agonist, and GABAB2, which activates G proteins, as a model system. By using a novel orthogonal-labelling approach compatible with time-resolved FRET and based on ACP- and SNAP-tag technologies to verify the heterodimerization of wild-type and mutated GABAB subunits, we demonstrate the existence of a direct allosteric coupling between the 7TMs of GABAB heterodimers. Indeed, a GABAB receptor, in which the GABAB2 extracellular domain was deleted, was still capable of activating G proteins. Furthermore, synthetic ligands for the GABAB2 7TM could increase agonist affinity at the GABAB1 subunit in this mutated receptor. In addition to bringing new information on GABAB receptor activation, these data clearly demonstrate the existence of direct trans-activation between the 7TM of two interacting proteins.
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Affiliation(s)
- Carine Monnier
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Département de Pharmacologie Moléculaire, Montpellier, France
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