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Liu Y, Singharoy A, Mayne CG, Sengupta A, Raghavachari K, Schulten K, Flood AH. Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles. J Am Chem Soc 2016; 138:4843-4851. [PMID: 27014837 PMCID: PMC4957974 DOI: 10.1021/jacs.6b00712] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Shape-persistent macrocycles are attractive functional targets for synthesis, molecular recognition, and hierarchical self-assembly. Such macrocycles are noncollapsible and geometrically well-defined, and they are traditionally characterized by having repeat units and low conformational flexibility. Here, we find it necessary to refine these ideas in the face of highly flexible yet shape-persistent macrocycles. A molecule is shape-persistent if it has a small change in shape when perturbed by external stimuli (e.g., heat, light, and redox chemistry). In support of this idea, we provide the first examination of the relationships between a macrocycle's shape persistence, its conformational space, and the resulting functions. We do this with a star-shaped macrocycle called cyanostar that is flexible as well as being shape-persistent. We employed molecular dynamics (MD), density functional theory (DFT), and NMR experiments. Considering a thermal bath as a stimulus, we found a single macrocycle has 332 accessible conformers with olefins undergoing rapid interconversion by up-down and in-out motions on short time scales (0.2 ns). These many interconverting conformations classify single cyanostars as flexible. To determine and confirm that cyanostars are shape-persistent, we show that they have a high 87% shape similarity across these conformations. To further test the idea, we use the binding of diglyme to the single macrocycle as guest-induced stimulation. This guest has almost no effect on the conformational space. However, formation of a 2:1 sandwich complex involving two macrocycles enhances rigidity and dramatically shifts the conformer distribution toward perfect bowls. Overall, the present study expands the scope of shape-persistent macrocycles to include flexible macrocycles if, and only if, their conformers have similar shapes.
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Affiliation(s)
- Yun Liu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, USA
| | - Christopher G. Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, USA
| | - Arkajyoti Sengupta
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | - Amar H. Flood
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
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Luber S, Herrmann C, Reiher M. Relevance of the Electric-Dipole−Electric-Quadrupole Contribution to Raman Optical Activity Spectra. J Phys Chem B 2008; 112:2218-32. [DOI: 10.1021/jp0756404] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Sandra Luber
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - Carmen Herrmann
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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Bernatowicz P, Kowalewski J, Szymanski S. Nuclear-spin relaxation in nonrigid molecules: discrete multisite local dynamics combined with anisotropic molecular reorientation. J Chem Phys 2007; 124:024108. [PMID: 16422572 DOI: 10.1063/1.2149858] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nuclear-spin relaxation is considered in a molecular system undergoing two types of dynamic processes: asymmetric-top small-step rotational diffusion and discrete multisite local jumps. The two processes are assumed to be uncorrelated. Time correlation functions for relevant rank-two interactions and corresponding spectral density functions are derived for a general relation between the characteristic rate constants. In addition, limiting cases of fast and slow local motions and of some specific jump conditions are also investigated.
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Affiliation(s)
- Piotr Bernatowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
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4
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Bento ES, Calixto JB, Hawkes GE, Pizzolatti MG, Sant'Ana AEG, Yunes RA. The structure of velutinol A is (15R,16R,20S)-14,16:15,20:16,21-triepoxy-15,16-seco-14β,17α-pregn-5-ene-3β,15-dioul. A combined quantitative Overhauser effect and molecular modelling study. ACTA ACUST UNITED AC 1996. [DOI: 10.1039/p29960001359] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Peters T, Meyer B, Stuike-Prill R, Somorjai R, Brisson JR. A Monte Carlo method for conformational analysis of saccharides. Carbohydr Res 1993; 238:49-73. [PMID: 8431939 DOI: 10.1016/0008-6215(93)87005-d] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A Metropolis Monte Carlo (MMC) algorithm was applied to explore conformational spaces spanned by the exocyclic dihedral angles of four disaccharides alpha-D-Man(1-->3)-alpha-D-Man(1-->O)Me (1), alpha-D-Man(1-->2)-alpha-D-Man(1-->O)Me (2), methyl beta-cellobioside (3), and methyl beta-maltoside (4). The simulation method uses the HSEA force field and randomly samples the conformational space with an automatic preference for low-energy states. In comparison to a systematic grid search, MMC offers a much more convenient and efficient protocol for the computation of ensemble average values of experimentally accessible NMR parameters such as NOE effects or 3J coupling constants. Energy barriers of a few kcal/mol were found to be surmounted easily when running the simulations with the temperature parameter set at room temperature, whereas passing significantly higher barriers required elevated temperature parameters. Ensemble average NOE values were calculated using the MMC technique and a conventional systematic grid search showing that the MMC method adequately samples the conformational spaces of 1-4. Theoretical NOEs derived for global or local minimum conformations are different from ensemble average values, and it is shown that averaged NOEs agree significantly better with experimental data. Ensemble average NOEs for 1 derived from MMC/HSEA, and previously reported MM2CARB and AMBER calculations all showed good agreement with experimental data, with MMC/HSEA giving the closest fit.
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Affiliation(s)
- T Peters
- Institute for Biophysical Chemistry, University of Frankfurt, Germany
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6
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Kobayashi S, Onozawa SY, Mukaiyama T. An Efficient Synthesis of 6-Deoxy-D-allose from Simple Achiral Starting Materials. CHEM LETT 1992. [DOI: 10.1246/cl.1992.2419] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Baleja JD, Germann MW, van de Sande JH, Sykes BD. Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. J Mol Biol 1990; 215:411-28. [PMID: 2231713 DOI: 10.1016/s0022-2836(05)80361-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The solution structures of two alternating purine-pyrimidine octamers, [d(G-T-A-C-G-T-A-C)]2 and the reverse sequence [d(C-A-T-G-C-A-T-G)]2, are investigated by using nuclear magnetic resonance spectroscopy and restrained molecular dynamics calculations. Chemical shift assignments are obtained for non-exchangeable protons by a combination of two-dimensional correlation and nuclear Overhauser enhancement (NOE) spectroscopy experiments. Distances between protons are estimated by extrapolating distances derived from time-dependent NOE measurements to zero mixing time. Approximate dihedral angles are determined within the deoxyribose ring from coupling constants observed in one and two-dimensional spectra. Sets of distance and dihedral determinations for each of the duplexes form the bases for structure determination. Molecular dynamics is then used to generate structures that satisfy the experimental restraints incorporated as effective potentials into the total energy. Separate runs start from classical A and B-form DNA and converge to essentially identical structures. To circumvent the problems of spin diffusion and differential motion associated with distance measurements within molecules, models are improved by NOE-based refinement in which observed NOE intensities are compared to those calculated using a full matrix analysis procedure. The refined structures generally have the global features of B-type DNA. Some, but not all, variations in dihedral angles and in the spatial relationships of adjacent base-pairs are observed to be in synchrony with the alternating purine-pyrimidine sequence.
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Affiliation(s)
- J D Baleja
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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Baleja JD, Moult J, Sykes BD. Distance measurement and structure refinement with NOE data. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0022-2364(90)90015-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kay LE, Prestegard J. Spin-lattice relaxation rates of coupled spins from 2D accordion spectroscopy. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0022-2364(88)90021-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Samitov YY, Sadykov RK. Stereospecificity in the proton magnetic relaxation rate of enantiotopic methyls and the methyl rotation barrier. THEOR EXP CHEM+ 1987. [DOI: 10.1007/bf00522544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Dais P, Perlin AS. Proton spin-lattice relaxation rates in the structural analysis of carbohydrate molecules in solution. Adv Carbohydr Chem Biochem 1987; 45:125-68. [PMID: 2829511 DOI: 10.1016/s0065-2318(08)60138-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- P Dais
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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Kövér KE. A simple method for selective saturation of multiplets in 1H-{1H} NOE measurements. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/0022-2364(84)90082-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Lee L, Sykes BD. Use of lanthanide-induced nuclear magnetic resonance shifts for determination of protein structure in solution: EF calcium binding site of carp parvalbumin. Biochemistry 1983; 22:4366-73. [PMID: 6626506 DOI: 10.1021/bi00288a004] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The binding of the paramagnetic lanthanide ion ytterbium to the calcium binding protein carp parvalbumin results in a series of 1H NMR resonances which are shifted far outside the envelope of the 1H NMR spectrum of the diamagnetic form of the protein; bound Yb3+ also induces shifts in the 13C NMR spectrum of parvalbumin and in the 113Cd NMR spectrum of cadmium-substituted parvalbumin. The interpretation of these lanthanide-shifted resonances in terms of the structure of the protein surrounding the metal binding site requires the determination of the orientation and principal elements of the magnetic susceptibility tensor of the protein-bound Yb3+ ion. A previous comparison [Lee, L., & Sykes, B. D. (1982) Biomolecular Structure Determination by NMR (Bothner-By, A. A., Glickson, J. D., & Sykes, B. D., Eds.) pp 169-188, Marcel Dekker, New York] of the observed Yb3+-shifted 1H NMR spectrum of parvalbumin with a calculated spectrum, based upon the X-ray structure and an initial determination of the magnetic susceptibility tensor, led to the conclusion that there were significant differences between the solution and X-ray structures. In this paper, the magnetic susceptibility tensor has been reevaluated with the aid of newly assigned 13C and 113Cd NMR resonances. The agreement between the calculated and observed spectra is now close overall.
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Bock K, Defaye J, Driguez H, Bar-Guilloux E. Conformations in solution of alpha,alpha-trehalose, alpha-D-glucopyranosyl alpha-D-mannopyranoside, and their 1-thioglycosyl analogs, and a tentative correlation of their behaviour with respect to the enzyme trehalase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 131:595-600. [PMID: 6840069 DOI: 10.1111/j.1432-1033.1983.tb07304.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The conformation in solution of alpha-D-glucopyranosyl alpha-D-glucopyranoside (alpha,alpha-trehalose, 1), alpha-D-glucopyranosyl alpha-D-mannopyranoside (3) and their corresponding 1-thioglycosyl analogs, alpha-D-glucopyranosyl 1-thio-alpha-D-glucopyranoside (1-thio-alpha,alpha-trehalose, 2) and alpha-D-glucopyranosyl 1-thio-alpha-D-mannopyranoside (4) were established from high-resolution 1H-NMR and 13C-NMR measurements. These experimental results are in good agreement with the conformations as inferred from hard-sphere calculations. The dihedral angles phi H and psi H are not significantly different for the O-glycosyl disaccharides 1 and 3 compared with their 1-thioglycosyl analogs 2 and 4; however, the internuclear H-1--H-1' and H-1--H-5' distances appear to be longer for 1-thiodisaccharides. This may account for the differences in affinities of cockchafer trehalase which have been observed. This enzyme exhibits less affinity for the competitive inhibitor alpha-D-glucopyranosyl 1-thio-alpha-D-mannopyranoside (4) than for its O-glycosyl analog 3 (Ki 0.055 mM versus 0.0057 mM). From the similarity in Ki between 1-thio-alpha, alpha-trehalose and alpha-D-glucopyranosyl 1-thio-alpha-D-mannopyranoside (0.050 mM versus 0.055 mM), it is possible to assume a similar decrease in the enzymic affinity between the natural substrate (1) and the corresponding 1-thioglycosyl inhibitor (2), which can together be ascribed to the aforementioned difference in the conformation of the molecules.
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Abstract
The nuclear Overhauser effect (NOE) leads to changes in the intensity of signal(s) of a set of nuclei as a function of their respective distances. The use of NOE allows to obtain structural informations on peptides and proteins in solution as well as the study of interactions between small ligands and biomolecules. In this review, aspects of the basic theory of the NOE will be presented and the more recent applications of homonuclear and heteronuclear NOE's in biomolecules will be surveyed. Typical examples will be illustrated and limitations of the method will be discussed.
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18
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Tropp J. Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J Chem Phys 1980. [DOI: 10.1063/1.439059] [Citation(s) in RCA: 273] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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A 1H nuclear magnetic relaxation study of the mechanism and solvent dependence of the motion of predominantly syndiotactic poly(methyl methacrylate) in dilute solution. POLYMER 1980. [DOI: 10.1016/0032-3861(80)90006-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
The evidence that reverse turns frequently occur as structural components of proteins, as well as of linear and cyclic peptides, is overwhelming. This review summarizes and examines critically the experimental evidence derived from physical methods such as 1H and 13C nuclear magnetic resonance spectroscopy, spin-lattice relaxation time, circular dichroism, IR spectroscopy, and X-ray crystallography. Secondly, theoretical evidence obtained from energy calculations, which rely on empirical energy functions, and correlative methods, which rely on algorithms based on the frequency of occurrence of amino acids, is evaluated. In particular, those theoretical studies for which complementary physical studies have been completed are emphasized. Finally, examples of structure-function relationships involving reverse turns and their biological recognition are demonstrated.
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Heatley F, Wood B. A proton magnetic relaxation study of the mechanism and solvent dependence of the molecular motion of polystyrene in dilute solution. POLYMER 1978. [DOI: 10.1016/0032-3861(78)90092-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Bergeron R, Rowan R. The molecular disposition of sodium p-nitrophenolate in the cavities of cycloheptaamylose and cyclohexaamylose in solution. Bioorg Chem 1976. [DOI: 10.1016/0045-2068(76)90027-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Hull WE, Sykes BD. Dipolar nuclear spin relaxation of19F in multispin systems. Application to19F labeled proteins. J Chem Phys 1975. [DOI: 10.1063/1.431367] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Breitmaier E, Spohn KH, Berger S. 13C-Spin-Gitter-Relaxationszeiten und die Beweglichkeit gelöster organischer Moleküle. Angew Chem Int Ed Engl 1975. [DOI: 10.1002/ange.19750870503] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Breitmaier E, Spohn KH, Berger S. 13C Spin-Lattice Relaxation Times and the Mobility of Organic Molecules in Solution. ACTA ACUST UNITED AC 1975. [DOI: 10.1002/anie.197501441] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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