1
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Ettich J, Wittich C, Moll JM, Behnke K, Floss DM, Reiners J, Christmann A, Lang PA, Smits SHJ, Kolmar H, Scheller J. Respiratory syncytial virus-approved mAb Palivizumab as ligand for anti-idiotype nanobody-based synthetic cytokine receptors. J Biol Chem 2023; 299:105270. [PMID: 37734558 PMCID: PMC10630626 DOI: 10.1016/j.jbc.2023.105270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Synthetic cytokine receptors can modulate cellular functions based on an artificial ligand to avoid off-target and/or unspecific effects. However, ligands that can modulate receptor activity so far have not been used clinically because of unknown toxicity and immunity against the ligands. Here, we developed a fully synthetic cytokine/cytokine receptor pair based on the antigen-binding domain of the respiratory syncytial virus-approved mAb Palivizumab as a synthetic cytokine and a set of anti-idiotype nanobodies (AIPVHH) as synthetic receptors. Importantly, Palivizumab is neither cross-reactive with human proteins nor immunogenic. For the synthetic receptors, AIPVHH were fused to the activating interleukin-6 cytokine receptor gp130 and the apoptosis-inducing receptor Fas. We found that the synthetic cytokine receptor AIPVHHgp130 was efficiently activated by dimeric Palivizumab single-chain variable fragments. In summary, we created an in vitro nonimmunogenic full-synthetic cytokine/cytokine receptor pair as a proof of concept for future in vivo therapeutic strategies utilizing nonphysiological targets during immunotherapy.
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Affiliation(s)
- Julia Ettich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christoph Wittich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jens M Moll
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany; PROvendis GmbH, Muelheim an der Ruhr, Germany
| | - Kristina Behnke
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Doreen M Floss
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jens Reiners
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Christmann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Philipp A Lang
- Institute of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Center for Structural Studies, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany; Centre of Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
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Sprague DJ, Getschman AE, Fenske TG, Volkman BF, Smith BC. Trisubstituted 1,3,5-Triazines: The First Ligands of the sY12-Binding Pocket on Chemokine CXCL12. ACS Med Chem Lett 2021; 12:1773-1782. [PMID: 34795867 PMCID: PMC8592115 DOI: 10.1021/acsmedchemlett.1c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
![]()
CXCL12, a CXC-type
chemokine, binds its receptor CXCR4, and the
resulting signaling cascade is essential during development and subsequently
in immune function. Pathologically, the CXCL12–CXCR4 signaling
axis is involved in many cancers and inflammatory diseases and thus
has sparked continued interest in the development of therapeutics.
Small molecules targeting CXCR4 have had mixed results in clinical
trials. Alternatively, small molecules targeting the chemokine instead
of the receptor provide a largely unexplored space for therapeutic
development. Here we report that trisubstituted 1,3,5-triazines are
competent ligands for the sY12-binding pocket of CXCL12. The initial
hit was optimized to be more synthetically tractable. Fifty unique
triazines were synthesized, and the structure–activity relationship
was probed. Using computational modeling, we suggest key structural
interactions that are responsible for ligand–chemokine binding.
The lipophilic ligand efficiency was improved, resulting in more soluble,
drug-like molecules with chemical handles for future development and
structural studies.
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Affiliation(s)
- Daniel J. Sprague
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Anthony E. Getschman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Tyler G. Fenske
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F. Volkman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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3
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Joodaki F, Martin LM, Greenfield ML. Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling. Phys Chem Chem Phys 2019; 21:23943-23965. [PMID: 31596287 DOI: 10.1039/c9cp04798k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tryptophan and tyrosine are amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic heteroaromatic rings. Employing appropriate heteroaromatic molecular structures is essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine. Geometric analysis and dynamics quantified how aromatic rings deviated from planar structures and exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance because the extent of ring planarity slightly affected local water concentrations near aromatic rings. Instantaneous all-atom normal mode analysis (NMA) and Fourier transformation of time autocorrelation functions of out-of-plane displacements were applied to study out-of-plane vibrations of atoms in these rings. The NMA started with minimum energy configurations and then averaged over fluctuations in aqueous solution. The frequencies and frequency patterns that were obtained for tryptophan and tyrosine with CHARMM36 differed from literature reports of Raman spectra, infrared spectra, and frequencies calculated using quantum mechanics, with some out-of-plane modes found at higher frequencies. Effects of imposing improper torsion potentials and changing torsion angle force constants were investigated for all atoms in the rings of tryptophan and tyrosine. Results show that these coarse force field variations only affect planarity and out-of-plane vibrations of atoms within the rings, and not other vibrations. Although increasing improper torsion force constants reduced deviations from aromatic ring planarity significantly, it increased out-of-plane mode frequencies. Reducing torsion angle force constants (with and without improper torsions) shifted modes to lower frequencies. A combination of decreasing most torsion angle force constants for ring atoms in both amino acids and including improper torsion forces attained frequencies and frequency patterns for out-of-plane normal modes that were more similar to the literature spectra. These force field variations decreased the extents of out-of-plane vibrations within the heteroaromatic rings of tryptophan, especially around the nitrogen atom in the ring, but not within the heteroaromatic ring of tyrosine. Conclusions were unaffected by the peptide endgroup, water, or simulation ensemble.
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Affiliation(s)
- Faramarz Joodaki
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, USA.
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5
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Lobysheva E, Taylor CM, Marshall GR, Kisselev OG. Tauroursodeoxycholic acid binds to the G-protein site on light activated rhodopsin. Exp Eye Res 2018; 170:51-57. [PMID: 29454859 PMCID: PMC5983371 DOI: 10.1016/j.exer.2018.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
The heterotrimeric G-protein binding site on G-protein coupled receptors remains relatively unexplored regarding its potential as a new target of therapeutic intervention or as a secondary site of action by the existing drugs. Tauroursodeoxycholic acid bears structural resemblance to several compounds that were previously identified to specifically bind to the light-activated form of the visual receptor rhodopsin and to inhibit its activation of transducin. We show that TUDCA stabilizes the active form of rhodopsin, metarhodopsin II, and does not display the detergent-like effects of common amphiphilic compounds that share the cholesterol scaffold structure, such as deoxycholic acid. Computer docking of TUDCA to the model of light-activated rhodopsin revealed that it interacts using similar mode of binding to the C-terminal domain of transducin alpha subunit. The ring regions of TUDCA made hydrophobic contacts with loop 3 region of rhodopsin, while the tail of TUDCA is exposed to solvent. The results show that TUDCA interacts specifically with rhodopsin, which may contribute to its wide-ranging effects on retina physiology and as a potential therapeutic compound for retina degenerative diseases.
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Affiliation(s)
- E Lobysheva
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - C M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - G R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - O G Kisselev
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
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6
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Pinheiro S, Soteras I, Gelpí JL, Dehez F, Chipot C, Luque FJ, Curutchet C. Structural and energetic study of cation–π–cation interactions in proteins. Phys Chem Chem Phys 2017; 19:9849-9861. [DOI: 10.1039/c6cp08448f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Statistical and energetic analysis of cation–π–cation motifs in protein structures suggests a potential stabilizing role in the protein fold.
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Affiliation(s)
- Silvana Pinheiro
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Barcelona
- Spain
| | - Ignacio Soteras
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Santa Coloma de Gramenet
- Spain
| | - Josep Lluis Gelpí
- Departament de Bioquímica i Biomedicina Molecular
- Facultat de Biologia
- Universitat de Barcelona
- Spain
| | - François Dehez
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana – Champaign
- Unité Mixte de Recherche No. 7565
- Université de Lorraine
- Vandoeuvre-lès-Nancy cedex
- France
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana – Champaign
- Unité Mixte de Recherche No. 7565
- Université de Lorraine
- Vandoeuvre-lès-Nancy cedex
- France
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Santa Coloma de Gramenet
- Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Barcelona
- Spain
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Tu T, Li Y, Su X, Meng K, Ma R, Wang Y, Yao B, Lin Z, Luo H. Probing the role of cation-π interaction in the thermotolerance and catalytic performance of endo-polygalacturonases. Sci Rep 2016; 6:38413. [PMID: 27929074 PMCID: PMC5143973 DOI: 10.1038/srep38413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
Understanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparent Tms increased by 0.6-3.9 °C) and catalytic efficiency (by up to 32-fold). Chromatogram analysis of the hydrolysis products indicated that a larger amount of shorter sugars were released from the polygalacturonic acid by these three mutants than by the wild-type. MD analysis of the enzyme-substrate complexes illustrated that the mutants with introduced cation-π interaction have modified conformations of catalytic crevice, which provide an enviable environment for the catalytic process. Moreover, the lower plasticity of T3 loop 2 at the edge of the subsite tunnel appears to recruit the reducing ends of oligogalacturonide into the active site tunnel and initiates new hydrolysis reactions. This study demonstrates the importance of cation-π interaction in protein conformation and provides a realistic strategy to enhance the thermotolerance and catalytic performance of endo-polygalacturonases.
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Affiliation(s)
- Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yeqing Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhemin Lin
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
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8
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Conformational Ensemble of hIAPP Dimer: Insight into the Molecular Mechanism by which a Green Tea Extract inhibits hIAPP Aggregation. Sci Rep 2016; 6:33076. [PMID: 27620620 PMCID: PMC5020610 DOI: 10.1038/srep33076] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/18/2016] [Indexed: 12/20/2022] Open
Abstract
Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a green tea extract, was found to inhibit hIAPP fibrillation. However, the inhibition mechanism and the conformational distribution of the smallest hIAPP oligomer – dimer are mostly unknown. Herein, we performed extensive replica exchange molecular dynamic simulations on hIAPP dimer with and without EGCG molecules. Extended hIAPP dimer conformations, with a collision cross section value similar to that observed by ion mobility-mass spectrometry, were observed in our simulations. Notably, these dimers adopt a three-stranded antiparallel β-sheet and contain the previously reported β-hairpin amyloidogenic precursor. We find that EGCG binding strongly blocks both the inter-peptide hydrophobic and aromatic-stacking interactions responsible for inter-peptide β-sheet formation and intra-peptide interaction crucial for β-hairpin formation, thus abolishes the three-stranded β-sheet structures and leads to the formation of coil-rich conformations. Hydrophobic, aromatic-stacking, cation-π and hydrogen-bonding interactions jointly contribute to the EGCG-induced conformational shift. This study provides, on atomic level, the conformational ensemble of hIAPP dimer and the molecular mechanism by which EGCG inhibits hIAPP aggregation.
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9
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Perera GS, Nettles CB, Zhou Y, Zou S, Hollis TK, Zhang D. Direct Observation of Ion Pairing at the Liquid/Solid Interfaces by Surface Enhanced Raman Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8998-9005. [PMID: 26258255 DOI: 10.1021/acs.langmuir.5b01903] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ion-pairing, the association of oppositely charged ionic species in solution and at liquid/solid interfaces has been proposed as a key factor for a wide range of physicochemical phenomena. However, experimental observations of ion pairing at the ligand/solid interfaces are challenging due to difficulties in differentiating ion species in the electrical double layer from that adsorbed on the solid surfaces. Using surface enhanced Raman spectroscopy in combination with electrolyte washing, we presented herein the first direct experimental evidence of ion pairing, the coadsorption of oppositely charged ionic species onto gold nanoparticles (AuNPs). Ion pairing reduces the electrolyte concentration threshold in inducing AuNP aggregation and enhances the competitiveness of electrolyte over neutral molecules for binding to AuNP surfaces. The methodology and insights provided in this work should be important for understanding electrolyte interfacial interactions with nanoparticles.
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Affiliation(s)
- Ganganath S Perera
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Charles B Nettles
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Yadong Zhou
- Department of Chemistry, University of Central Florida , Orlando, Florida 32816, United States
| | - Shengli Zou
- Department of Chemistry, University of Central Florida , Orlando, Florida 32816, United States
| | - T Keith Hollis
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Dongmao Zhang
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
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Myslinski JM, Clements JH, Martin SF. Protein-ligand interactions: probing the energetics of a putative cation-π interaction. Bioorg Med Chem Lett 2014; 24:3164-7. [PMID: 24856058 DOI: 10.1016/j.bmcl.2014.04.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/01/2023]
Abstract
In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion, binding free energies, ΔG°, for derivatives of RCO-pTyr-Ac6c-Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.
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Affiliation(s)
- James M Myslinski
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - John H Clements
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - Stephen F Martin
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA.
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Effect of stepwise microhydration on the guanidinium···π interaction. J Mol Model 2014; 20:2209. [PMID: 24691534 DOI: 10.1007/s00894-014-2209-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
The characteristics of the interaction of microhydrated guanidinium cation with the aromatic moieties present in the aromatic amino acids side chains have been studied by means of computational methods. The most stable minima found for non-hydrated complexes correspond in all cases to structures with guanidinium oriented toward the ring and interacting by means of N-H···π hydrogen bonds. The interaction becomes stronger when going from benzene (-14 kcal mol⁻¹) to phenol (-17 kcal mol⁻¹) to indole (-21 kcal mol⁻¹). These complexes are held together mainly by electrostatics, but with important contributions from induction and dispersion. The presence of a small number of water molecules significantly affects the characteristics of the complexes. Hydrogen bonds formed by water with the cation, another water molecule, or the aromatic units become more and more similar in intensity as water molecules are included in the complex, leading to a great variety of minima with similar stability but showing very different structural patterns. The behavior is similar with the three aromatic units, the differences in stability mainly being a consequence of the different strength of the cation···π contact.
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Affiliation(s)
- Ana A Rodríguez-Sanz
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo. Avda. Alfonso X El Sabio s/n, 27002, Lugo, Spain
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Mitra M, Manna P, Seth SK, Das A, Meredith J, Helliwell M, Bauzá A, Choudhury SR, Frontera A, Mukhopadhyay S. Salt-bridge–π (sb–π) interactions at work: associative interactions of sb–π, π–π and anion–π in Cu(ii)-malonate–2-aminopyridine–hexafluoridophosphate ternary system. CrystEngComm 2013. [DOI: 10.1039/c2ce26790j] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 719] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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14
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Campo-Cacharrón A, Cabaleiro-Lago EM, Rodríguez-Otero J. Effects of microhydration on the characteristics of cation–phenol complexes. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1290-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zheng X, Wu C, Ponder JW, Marshall GR. Molecular dynamics of β-hairpin models of epigenetic recognition motifs. J Am Chem Soc 2012; 134:15970-8. [PMID: 22934656 DOI: 10.1021/ja306803v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The conformations and stabilities of the β-hairpin model peptides of Waters (Riemen, A. J.; Waters, M. L. Biochemistry 2009, 48, 1525; Hughes, R. M.; Benshoff, M. L.; Waters, M. L. Chemistry 2007, 13, 5753) have been experimentally characterized as a function of lysine ε-methylation. These models were developed to explore molecular recognition of known epigenetic recognition motifs. This system offered an opportunity to computationally examine the role of cation-π interactions, desolvation of the ε-methylated ammonium groups, and aromatic/aromatic interactions on the observed differences in NMR spectra. AMOEBA, a second-generation force field (Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr.; Head-Gordon, M.; Clark, G. N.; Johnson, M. E.; Head-Gordon, T. J. Phys. Chem. B 2010, 114, 2549), was chosen as it includes both multipole electrostatics and polarizability thought to be essential to accurately characterize such interactions. Independent parametrization of ε-methylated amines was required from which aqueous solvation free energies were estimated and shown to agree with literature values. Molecular dynamics simulations (100 ns) using the derived parameters with model peptides, such as Ac-R-W-V-W-V-N-G-Orn-K(Me)(n)-I-L-Q-NH(2), where n = 0, 1, 2, or 3, were conducted in explicit solvent. Distances between the centers of the indole rings of the two-tryptophan residues, 2 and 4, and the ε-methylated ammonium group on Lys-9 as well as the distance between the N- and C-termini were monitored to estimate the strength and orientation of the cation-π and aromatic/aromatic interactions. In agreement with the experimental data, the stability of the β-hairpin increased significantly with lysine ε-methylation. The ability of MD simulations to reproduce the observed NOEs for the four peptides was further estimated for the monopole-based force fields, AMBER, CHARMM, and OPLSAA. AMOEBA correctly predicted over 80% of the observed NOEs for all 4 peptides, while the three-monopole force fields were 40-50% predictive in only 2 cases and approximately 10% in the other 10 examples. Preliminary analysis suggests that the decreased cost of desolvation of the substituted ammonium group significantly compensated for the reduced cation-π interaction resulting from the increased separation due to steric bulk of the ε-methylated amines.
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Affiliation(s)
- Xiange Zheng
- Department of Chemistry and of Biochemistry, Washington University, St. Louis, Missouri 63105, United States
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Effect of stepwise microhydration on the methylammonium···phenol and ammonium···phenol interaction. J Mol Model 2012; 19:1985-94. [DOI: 10.1007/s00894-012-1579-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
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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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19
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Campo-Cacharrón A, Cabaleiro-Lago EM, Rodríguez-Otero J. A DFT Study of the Interaction between Microhydrated Anions and Naphthalendiimides. Chemphyschem 2011; 13:570-7. [DOI: 10.1002/cphc.201100678] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Indexed: 12/17/2022]
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20
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Cabaleiro-Lago EM, Rodríguez-Otero J, Peña-Gallego Á. Effect of microhydration on the guanidinium⋯benzene interaction. J Chem Phys 2011; 135:214301. [DOI: 10.1063/1.3663277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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21
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Nomura T, Kamada R, Ito I, Sakamoto K, Chuman Y, Ishimori K, Shimohigashi Y, Sakaguchi K. Probing phenylalanine environments in oligomeric structures with pentafluorophenylalanine and cyclohexylalanine. Biopolymers 2011; 95:410-9. [PMID: 21280026 DOI: 10.1002/bip.21594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Stabilization of protein structures and protein-protein interactions are critical in the engineering of industrially useful enzymes and in the design of pharmaceutically valuable ligands. Hydrophobic interactions involving phenylalanine residues play crucial roles in protein stability and protein-protein/peptide interactions. To establish an effective method to explore the hydrophobic environments of phenylalanine residues, we present a strategy that uses pentafluorophenylalanine (F5Phe) and cyclohexylalanine (Cha). In this study, substitution of F5Phe or Cha for three Phe residues at positions 328, 338, and 341 in the tetramerization domain of the tumor suppressor protein p53 was performed. These residues are located at the interfaces of p53-p53 interactions and are important in the stabilization of the tetrameric structure. The stability of the p53 tetrameric structure did not change significantly when F5Phe-containing peptides at positions Phe328 or Phe338 were used. In contrast, the substitution of Cha for Phe341 in the hydrophobic core enhanced the stability of the tetrameric structure with a T(m) value of 100 degrees C. Phe328 and Phe338 interact with each other through pi-interactions, whereas Phe341 is buried in the surrounding alkyl side-chains of the hydrophobic core of the p53 tetramerization domain. Furthermore, high pressure-assisted denaturation analysis indicated improvement in the occupancy of the hydrophobic core. Considerable stabilization of the p53 tetramer was achieved by filling the identified cavity in the hydrophobic core of the p53 tetramer. The results indicate the status of the Phe residues, indicating that the "pair substitution" of Cha and F5Phe is highly suitable for probing the environments of Phe residues.
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Affiliation(s)
- Takao Nomura
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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22
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Sabatino D, Proulx C, Pohankova P, Ong H, Lubell WD. Structure–Activity Relationships of GHRP-6 Azapeptide Ligands of the CD36 Scavenger Receptor by Solid-Phase Submonomer Azapeptide Synthesis. J Am Chem Soc 2011; 133:12493-506. [DOI: 10.1021/ja203007u] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange New Jersey 07079, United States
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23
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Shim JY. Understanding functional residues of the cannabinoid CB1. Curr Top Med Chem 2011; 10:779-98. [PMID: 20370713 DOI: 10.2174/156802610791164210] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 10/27/2009] [Indexed: 02/07/2023]
Abstract
The brain cannabinoid (CB(1)) receptor that mediates numerous physiological processes in response to marijuana and other psychoactive compounds is a G protein coupled receptor (GPCR) and shares common structural features with many rhodopsin class GPCRs. For the rational development of therapeutic agents targeting the CB(1) receptor, understanding of the ligand-specific CB(1) receptor interactions responsible for unique G protein signals is crucial. For a more than a decade, a combination of mutagenesis and computational modeling approaches has been successfully employed to study the ligand-specific CB(1) receptor interactions. In this review, after a brief discussion about recent advances in understanding of some structural and functional features of GPCRs commonly applicable to the CB(1) receptor, the CB(1) receptor functional residues reported from mutational studies are divided into three different types, ligand binding (B), receptor stabilization (S) and receptor activation (A) residues, to delineate the nature of the binding pockets of anandamide, CP55940, WIN55212-2 and SR141716A and to describe the molecular events of the ligand-specific CB(1) receptor activation from ligand binding to G protein signaling. Taken these CB(1) receptor functional residues, some of which are unique to the CB(1) receptor, together with the biophysical knowledge accumulated for the GPCR active state, it is possible to propose the early stages of the CB(1) receptor activation process that not only provide some insights into understanding molecular mechanisms of receptor activation but also are applicable for identifying new therapeutic agents by applying the validated structure-based approaches, such as virtual high throughput screening (HTS) and fragment-based approach (FBA).
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Affiliation(s)
- Joong-Youn Shim
- J.L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA.
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24
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Contributions of cation–π interactions to the collagen triple helix stability. Arch Biochem Biophys 2011; 508:46-53. [DOI: 10.1016/j.abb.2011.01.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 01/07/2011] [Accepted: 01/12/2011] [Indexed: 11/20/2022]
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25
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Vivoli M, Angelucci F, Ilari A, Morea V, Angelaccio S, di Salvo ML, Contestabile R. Role of a conserved active site cation-pi interaction in Escherichia coli serine hydroxymethyltransferase. Biochemistry 2010; 48:12034-46. [PMID: 19883126 DOI: 10.1021/bi901568b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serine hydroxymethyltransferase is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the interconversion of serine and glycine using tetrahydropteroylglutamate as the one-carbon carrier. In all pyridoxal phosphate-dependent enzymes, amino acid substrates are bound and released through a transaldimination process, in which an internal aldimine and an external aldimine are interconverted via gem-diamine intermediates. Bioinformatic analyses of serine hydroxymethyltransferase sequences and structures showed the presence of two highly conserved residues, a tyrosine and an arginine, engaged in a cation-pi interaction. In Escherichia coli serine hydroxymethyltranferase, the hydroxyl group of this conserved tyrosine (Tyr55) is located in a position compatible with a role as hydrogen exchanger in the transaldimination reaction. Because of the location of Tyr55 at the active site, the enhancement of its acidic properties caused by the cation-pi interaction with Arg235, and the hydrogen bonds established by its hydroxyl group, a role of this residue as acid-base catalyst in the transaldimination process was envisaged. The role played by this cation-pi interaction in the E. coli serine hydroxymethyltransferase was investigated by crystallography and site-directed mutagenesis using Y55F and three R235 mutant forms. The crystal structure of the Y55F mutant suggests that the presence of Tyr55 is indispensable for a correct positioning of the cofactor and for the maintenance of the structure of several loops involved in substrate and cofactor binding. The kinetic properties of all mutant enzymes are profoundly altered. Substrate binding and rapid kinetic experiments showed that both Y55 and R235 are required for a correct progress of the transaldimination reaction.
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Affiliation(s)
- Mirella Vivoli
- Dipartimento di Scienze Biochimiche and Istituto Pasteur, Fondazione Cenci Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro, 5-00185 Roma, Italy
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26
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Taylor CM, Rockweiler NB, Liu C, Rikimaru L, Tunemalm AK, Kisselev OG, Marshall GR. Using ligand-based virtual screening to allosterically stabilize the activated state of a GPCR. Chem Biol Drug Des 2010; 75:325-32. [PMID: 20659113 DOI: 10.1111/j.1747-0285.2009.00944.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-protein coupled receptors play an essential role in many biological processes. Despite an increase in the number of solved X-ray crystal structures of G-protein coupled receptors, capturing a G-protein coupled receptor in its activated state for structural analysis has proven to be difficult. An unexplored paradigm is stabilization of one or more conformational states of a G-protein coupled receptor via binding a small molecule to the intracellular loops. A short tetrazole peptidomimetic based on the photoactivated state of rhodopsin-bound structure of Gt(alpha)(340-350) was previously designed and shown to stabilize the photoactivated state of rhodopsin, the G-protein coupled receptor involved in vision. A pharmacophore model derived from the designed tetrazole tetrapeptide was used for ligand-based virtual screening to enhance the possible discovery of novel scaffolds. Maybridge Hitfinder and National Cancer Institute diversity libraries were screened for compounds containing the pharmacophore. Forty-seven compounds resulted from virtually screening the Maybridge library, whereas no hits resulted with the National Cancer Institute library. Three of the 47 Maybridge compounds were found to stabilize the MII state. As these compounds did not inhibit binding of transducin to photoactivated state of rhodopsin, they were assumed to be allosteric ligands. These compounds are potentially useful for crystallographic studies where complexes with these compounds might capture rhodopsin in its activated conformational state.
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Affiliation(s)
- Christina M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO 63110, USA
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Abstract
Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
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Affiliation(s)
- Hans-Jörg Schneider
- Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken, Deutschland.
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29
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Neuwald AF. The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches. J Mol Biol 2009; 390:142-53. [PMID: 19427324 DOI: 10.1016/j.jmb.2009.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 04/07/2009] [Accepted: 05/01/2009] [Indexed: 11/19/2022]
Abstract
Ras-like GTPases function as on/off switches in intracellular signaling pathways. Their on or off state is communicated through conformational changes in the so-called switch I and II regions. It is commonly believed that the distinguishing molecular features of these GTPases are well known. Here, however, I identify-through a Bayesian iterative analysis of GTPase evolutionary divergence-a previously undescribed switch II structural component that (along with previously described, functionally critical residues) most distinguish these signaling pathway on/off switches from other GTPases. In certain Ras-like GTPases this newly-identified component forms an aromatic pocket around the negative-dipole moment at the end of a switch II helix with a positively charged residue inserted into the pocket. This helix is oriented in a specific direction away from the GTPase core, but is reoriented dramatically upon disruption of the charge-dipole pocket. The charge-dipole pocket occurs in both the on and off states and both the charge-dipole pocket and an alternative configuration occur within the unit cell of a single crystal structure of Rab5a GTPase in the off state. Thus, the charge-dipole pocket configuration is closely associated, not with the on or off state, but rather with formation of the outward-oriented helix and, as a result, with restructuring of the switch II N-terminal region, which has a critical role both in sensing the on/off state and in mediating GTP hydrolysis and nucleotide exchange.
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Affiliation(s)
- Andrew F Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, 21201, USA.
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30
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Salonen LM, Bucher C, Banner DW, Haap W, Mary JL, Benz J, Kuster O, Seiler P, Schweizer WB, Diederich F. Cation-pi interactions at the active site of factor Xa: dramatic enhancement upon stepwise N-alkylation of ammonium ions. Angew Chem Int Ed Engl 2009; 48:811-4. [PMID: 19101972 DOI: 10.1002/anie.200804695] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura M Salonen
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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31
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Salonen L, Bucher C, Banner D, Haap W, Mary JL, Benz J, Kuster O, Seiler P, Schweizer W, Diederich F. Kation-π-Wechselwirkungen im aktiven Zentrum von Faktor Xa: drastische Verstärkung durch stufenweise N-Alkylierung von Ammoniumionen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804695] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Gribbon C, Channon KJ, Zhang W, Banwell EF, Bromley EHC, Chaudhuri JB, Oreffo ROC, Woolfson DN. MagicWand: A Single, Designed Peptide That Assembles to Stable, Ordered α-Helical Fibers. Biochemistry 2008; 47:10365-71. [DOI: 10.1021/bi801072s] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christopher Gribbon
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Kevin J. Channon
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Weijie Zhang
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Eleanor F. Banwell
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Elizabeth H. C. Bromley
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Julian B. Chaudhuri
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Richard O. C. Oreffo
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K., Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, U.K., Bone and Joint Research Group, Institute of Developmental Sciences, University of Southampton, Southampton SO16 6YD, U.K., and Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, U.K
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33
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Taylor CM, Barda Y, Kisselev OG, Marshall GR. Modulating G-protein coupled receptor/G-protein signal transduction by small molecules suggested by virtual screening. J Med Chem 2008; 51:5297-303. [PMID: 18707087 DOI: 10.1021/jm800326q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modulation of interactions between activated GPCRs (G-protein coupled receptors) and the intracellular (IC) signal transducers, heterotrimeric G-proteins, is an attractive, yet essentially unexplored, paradigm for treatment of certain diseases. Regulating downstream signaling for treatment of congenital diseases due to constitutively active GPCRs, as well as tumors where GPCRs are often overexpressed, requires the development of new methodologies. Modeling, experimental data, docking, scoring, and experimental testing (MEDSET) was developed to discover inhibitors that target the IC loops of activated GPCRs. As proof-of-concept, MEDSET developed and utilized a model of the interface between photoactivated rhodopsin (R*) and transducin (Gt), its G-protein. A National Cancer Institute (NCI) compound library was screened to identify compounds that bound at the interface between R* and its G-protein. High-scoring compounds from this virtual screen were obtained and tested experimentally for their ability to stabilize R* and prevent Gt from binding to R*. Several compounds that modulate signal transduction have been identified.
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Affiliation(s)
- Christina M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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34
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Rana S, Kundu B, Durani S. A mixed-α,β miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine. Biopolymers 2007; 87:231-43. [PMID: 17879332 DOI: 10.1002/bip.20829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The protein-structure space is limited to L configuration in the asymmetric alpha-amino acid structures; the function space, on other hand, seems limitless because of the chemical diversity in the amino acid side chain structures. The chemical diversity in side chain structure may be multiplied beneficially with the stereochemical diversity in main chain structure; thus, de novo protein design may be explored for customizing molecular structures stereochemically and molecular functions chemically. Illustrating de novo design in the structure space of L and D alphabet, canonical all-beta folds of poly-L structure were reprogrammed as bracelet, boat, and canoe-shaped molecules-the "boat" as a receptor-like pocket and the "canoe" as a metal-ion receptor-simply by mutating specific L-amino acid residues to the corresponding D stereochemical structure. Demonstrating customization of molecular shape stereochemically and function chemically, a 15-residue mixed-alpha, beta miniprotein of canonical poly-L structure is now reprogrammed stereochemically as a cup-shaped receptor for acetylcholine via cation-pi interaction with a triad of aromatic side chains placed in mimicry of the acetylcholine-receptor sites both natural and artificial. Evidence from CD, fluorescence, NMR, DSC, ITC, MD, and molecular-docking studies is presented to show that a rationally designed 15-residue mixed-L, D peptide is a cooperatively ordered molecular fold in the stereochemically specified molecular morphology, submicromolar in affinity of acetylcholine and thus an acetylcholine receptor exceptionally small and simple. .
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Affiliation(s)
- Soumendra Rana
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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Taylor CM, Nikiforovich GV, Marshall GR. Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin. Biophys J 2007; 92:4325-34. [PMID: 17351008 PMCID: PMC1877773 DOI: 10.1529/biophysj.106.099242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Accepted: 01/30/2007] [Indexed: 12/26/2022] Open
Abstract
A novel combination of experimental data and extensive computational modeling was used to explore probable protein-protein interactions between photoactivated rhodopsin (R*) and experimentally determined R*-bound structures of the C-terminal fragment of alpha-transducin (Gt(alpha)(340-350)) and its analogs. Rather than using one set of loop structures derived from the dark-adapted rhodopsin state, R* was modeled in this study using various energetically feasible sets of intracellular loop (IC loop) conformations proposed previously in another study. The R*-bound conformation of Gt(alpha)(340-350) and several analogs were modeled using experimental transferred nuclear Overhauser effect data derived upon binding R*. Gt(alpha)(340-350) and its analogs were docked to various conformations of the intracellular loops, followed by optimization of side-chain spatial positions in both R* and Gt(alpha)(340-350) to obtain low-energy complexes. Finally, the structures of each complex were subjected to energy minimization using the OPLS/GBSA force field. The resulting residue-residue contacts at the interface between R* and Gt(alpha)(340-350) were validated by comparison with available experimental data, primarily from mutational studies. Computational modeling performed for Gt(alpha)(340-350) and its analogs when bound to R* revealed a consensus of general residue-residue interactions, necessary for efficient complex formation between R* and its Gt(alpha) recognition motif.
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Affiliation(s)
- Christina M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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36
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Dölker N, Deupi X, Pardo L, Campillo M. Charge-charge and cation-π interactions in ligand binding to G protein-coupled receptors. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0341-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Anderson MA, Ogbay B, Kisselev OG, Cistola DP, Marshall GR. Alternate Binding Mode of C-terminal Phenethylamine Analogs of Gt?(340?350) to Photoactivated Rhodopsin. Chem Biol Drug Des 2006; 68:295-307. [PMID: 17177891 DOI: 10.1111/j.1747-0285.2006.00460.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The C-terminus of the Galpha-subunit of transducin plays an important role in receptor recognition. Synthetic peptides corresponding to the last 11 residues of the subunit have been shown to stabilize the photoactivated form of rhodopsin, Rh*. The Rh*-bound structure of the G(t)alpha(340-350) peptide has been determined using transferred nuclear overhauser effect NMR. In that structure, we observed two interactions between Lys341 and Phe350, a cation-pi interaction between the epsilon-amine and the aromatic ring of Phe350 and a salt-bridge between the epsilon-amine and the C-terminal carboxylate. A series of C-terminal phenethylamine analogs of the G(t)alpha(340-350) peptide were synthesized, lacking the C-terminal carboxylate group, to investigate the forces that contribute to the stability of the Rh*-bound conformation of the peptide. Rh*-stabilization assay data suggest that the C-terminal carboxylate is not necessary to maintain binding affinity. Transferred nuclear overhauser effect NMR experiments reveal that these C-terminal phenethylamine peptides adopt an Rh*-bound structure that is similar overall, but lacking some of the intramolecular interactions observed in the native Rh*-bound G(t)alpha(340-350) structure. These studies suggest that the binding site for G(t)alpha(340-350) on Rh* is adaptable, and we propose that the charged carboxylate of Phe350 does not play a significant role in the interaction with Rh*, but helps stabilize the Rh*-bound confirmation of the native peptide.
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Affiliation(s)
- Matthew A Anderson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
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