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Berry SN, Zou M, Nguyen SL, Sajowitz AE, Qin L, Lewis W, Jolliffe KA. Supramolecular Control of the Temperature Responsiveness of Fluorescent Macrocyclic Molecular Rotamers. Chemistry 2024:e202400504. [PMID: 38499467 DOI: 10.1002/chem.202400504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
To fully harness the potential of molecular machines, it is crucial to develop methods by which to exert control over their speed of motion through the application of external stimuli. A conformationally strained macrocyclic fluorescent rotamer, CarROT, displays a reproducible and linear fluorescence decrease towards temperature over the physiological temperature range. Through the external addition of anions, cations or through deprotonation, the compound can access four discreet rotational speeds via supramolecular interactions (very slow, slow, fast and very fast) which in turn stop, reduce or enhance the thermoluminescent properties due to increasing or decreasing non-radiative decay processes, thereby providing a means to externally control the temperature sensitivity of the system. Through comparison with analogues with a higher degree of conformational freedom, the high thermosensitivity of CarROT over the physiological temperature range was determined to be due to conformational strain, which causes a high energy barrier to rotation over this range. Analogues with a higher degree of conformational freedom display lower sensitivities towards temperature over the same temperature range. This study provides an example of an information rich small molecule, in which programable rotational speed states can be observed with facile read-out.
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Affiliation(s)
- Stuart N Berry
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
| | - Meijun Zou
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
| | - Sarah L Nguyen
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
| | - Aidan E Sajowitz
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
| | - Lei Qin
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
| | - William Lewis
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
- Sydney Analytical, The University of Sydney, NSW, 2006, Australia
| | - Katrina A Jolliffe
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW, 2006, Australia
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2
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Platts JA, Kariuki BM, Newman PD. Welcoming Neighbour or Inhospitable Host? Selective Second Metal Binding in 5- and 6-Phospha-Substituted Bpy Ligands. Molecules 2024; 29:1150. [PMID: 38474663 DOI: 10.3390/molecules29051150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
The controlled formation of mixed-metal bimetallics was realised through use of a fac-[Re(CO)3(N,N'-bpy-P)Cl] complex bearing an exogenous 2,4,6-trioxa-1,3,5,7-tetramethyl-8-phosphaadamantane donor at the 5-position of the bpy. The introduction of gold, silver, and rhodium with appropriate secondary ligands was readily achieved from established starting materials. Restricted rotation about the C(bpy)-P bond was observed in several of the bimetallic complexes and correlated with the relative steric bulk of the second metal moiety. Related chemistry with the 6-substituted derivative proved more limited in scope with only the bimetallic Re/Au complex being isolated.
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Affiliation(s)
- James A Platts
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | | | - Paul D Newman
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
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3
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Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
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4
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Shendrikov VP, Alekseeva AS, Kot EF, Mineev KS, Tretiakova DS, Ece A, Boldyrev IA. Indane Based Molecular Motors: UV-Switching Increases Number of Isomers. Molecules 2022; 27:molecules27196716. [PMID: 36235252 PMCID: PMC9570826 DOI: 10.3390/molecules27196716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/01/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022] Open
Abstract
We describe azophenylindane based molecular motors (aphin-switches) which have two different rotamers of trans-configuration and four different rotamers of cis-configuration. The behaviors of these motors were investigated both experimentally and computationally. The conversion of aphin-switch does not yield single isomer but a mixture of these. Although the trans to cis conversion leads to the increase of the system entropy some of the cis-rotamers can directly convert to each other while others should convert via trans-configuration. The motion of aphin-switches resembles the work of a mixing machine with indane group serving as a base and phenol group serving as a beater. The aphin-switches presented herein may provide a basis for promising applications in advanced biological systems or particularly in cases where on demand disordering of molecular packing has value, such as lipid bilayers.
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Affiliation(s)
- Valeriy P. Shendrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Higher Chemical College, Mendeleev University of Chemical Technology of Russia, Miusskaya Sq. 9, 125047 Moscow, Russia
| | - Anna S. Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Erik F. Kot
- Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Daria S. Tretiakova
- Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul 34010, Turkey
| | - Ivan A. Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic, Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-495-330-66-10
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Pletzer M, Plasser F, Rimmele M, Heeney M, Glöcklhofer F. [2.2.2.2]Paracyclophanetetraenes (PCTs): cyclic structural analogues of poly( p‑phenylene vinylene)s (PPVs). Open Res Eur 2022; 1:111. [PMID: 37645175 PMCID: PMC10445936 DOI: 10.12688/openreseurope.13723.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/03/2022] [Indexed: 08/31/2023]
Abstract
Background: Poly( p-phenylene vinylene)s ( PPVs) and [2.2.2.2]paracyclophanetetraene ( PCT) are both composed of alternating π-conjugated para-phenylene and vinylene units. However, while the former constitute a class of π-conjugated polymers that has been used in organic electronics for decades, the latter is a macrocycle that only recently revealed its potential for applications such as organic battery electrodes. The cyclic structure endows PCT with unusual properties, and further tuning of these may be required for specific applications. Methods: In this article, we adopt an approach often used for tuning the properties of PPVs, the introduction of alkoxy (or alkylthio) substituents at the phenylene units, for tuning the optoelectronic properties of PCT. The resulting methoxy- and methylthio-substituted PCTs, obtained by Wittig cyclisation reactions, are studied by UV-vis absorption, photoluminescence, and cyclic voltammetry measurements, and investigated computationally using the visualisation of chemical shielding tensors (VIST) method. Results: The measurements show that substitution leads to slight changes in terms of absorption/emission energies and redox potentials while having a pronounced effect on the photoluminescence intensity. The computations show the effect of the substituents on the ring currents and chemical shielding and on the associated local and global (anti)aromaticity of the macrocycles, highlighting the interplay of local and global aromaticity in various electronic states. Conclusions: The study offers interesting insights into the tuneability of the properties of this versatile class of π-conjugated macrocycles.
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Affiliation(s)
- Matthias Pletzer
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
| | - Felix Plasser
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, UK
| | - Martina Rimmele
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
| | - Martin Heeney
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
| | - Florian Glöcklhofer
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Centre for Processable Electronics, Imperial College London, London, W12 0BZ, UK
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6
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Grinev VS, Mayorova OA, Anis’kova TV, Tikhomolova AS, Yegorova AY. Structure, Z' = 2 Crystal Packing Features of 3-(2-Chlorobenzylidene)-5-( p-tolyl)furan-2(3 H)-one. Molecules 2021; 26:2137. [PMID: 33917731 PMCID: PMC8068103 DOI: 10.3390/molecules26082137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 11/23/2022] Open
Abstract
3-(2-Chlorobenzylidene)-5-(p-tolyl)furan-2(3H)-one (1), C18H13ClO2, crystallizes with Z = 8 and Z' = 2, and the structure at 100 K has orthorhombic (Pna21) symmetry. Each kind of molecule takes part in π-π stacking interactions to form infinite chains parallel to the c axis. We believe that the existence of two forms can be explained by the probable rotation around a single C-C bond. The quantum chemical modeling reveals that these molecules are almost equivalent energetically, and they can be described as the two most stable conformers (rotamers) with a minor rotational barrier of about 0.67 kcal/mol.
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Affiliation(s)
- Vyacheslav S. Grinev
- Institute of Biochemistry and Physiology of Plants and Microorganisms RAS, Prospekt Entuziastov 13, 410049 Saratov, Russia;
- Institute of Chemistry, N.G. Chernyshevsky Saratov National Research State University, Ulitsa Astrakhanskaya 83, 410012 Saratov, Russia; (T.V.A.); (A.S.T.); (A.Y.Y.)
| | - Oksana A. Mayorova
- Institute of Biochemistry and Physiology of Plants and Microorganisms RAS, Prospekt Entuziastov 13, 410049 Saratov, Russia;
| | - Tatyana V. Anis’kova
- Institute of Chemistry, N.G. Chernyshevsky Saratov National Research State University, Ulitsa Astrakhanskaya 83, 410012 Saratov, Russia; (T.V.A.); (A.S.T.); (A.Y.Y.)
| | - Alexandra S. Tikhomolova
- Institute of Chemistry, N.G. Chernyshevsky Saratov National Research State University, Ulitsa Astrakhanskaya 83, 410012 Saratov, Russia; (T.V.A.); (A.S.T.); (A.Y.Y.)
| | - Alevtina Yu. Yegorova
- Institute of Chemistry, N.G. Chernyshevsky Saratov National Research State University, Ulitsa Astrakhanskaya 83, 410012 Saratov, Russia; (T.V.A.); (A.S.T.); (A.Y.Y.)
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7
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Szigetvári Á, Szántay C. On the utility of nonuniformly sampled two-dimensional NMR spectra in the pharmaceutical industry. Magn Reson Chem 2021; 59:264-286. [PMID: 32754953 DOI: 10.1002/mrc.5085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/14/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
In this work, we discuss representative examples of the application of nonuniform sampling (NUS) in small-molecule structure determination in a pharmaceutical research and development and quality control setting. We demonstrate the advantages of NUS over traditional sampling in various industrial applications of nuclear magnetic resonance (NMR). We propose an optimal trade-off between the quality and the time efficiency of 'routine' measurements, as demonstrated via a test sample of vinpocetine analyzed on a 'work horse' NMR spectrometer. In addition, we present case studies where the application of NUS contributed significantly to the successful completion of some challenging structure determination task at hand. To that end, in some cases, we combined NUS with a method of decoupling in the indirect dimension that gives 'constant time' nuclear Overhauser effect spectroscopy (NOESY) and 'constant time' heteronuclear multiple bond correlation (HMBC) spectra. NUS proved to be superior over traditional sampling even for the analysis of trace impurities, where the need to cope with a thousand-fold or even larger dynamic range and low signal-to-noise ratio for the impurity signals is quite a challenge.
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Affiliation(s)
- Áron Szigetvári
- Spectroscopic Research Department, Gedeon Richter Plc., Budapest, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc., Budapest, Hungary
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8
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Mames A, Gołowicz D, Pietrzak M, Kazimierczuk K, Szymański S, Ratajczyk T. Blue-Shift Hydrogen Bonds in Silyltriptycene Derivatives: Antibonding σ* Orbitals of the Si-C Bond as Effective Acceptors of Electron Density. Chemphyschem 2020; 21:540-545. [PMID: 31951312 DOI: 10.1002/cphc.201901141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/08/2020] [Indexed: 11/07/2022]
Abstract
Triptycene derivatives are widely utilized in different fields of chemistry and materials sciences. Their physicochemical properties, often of pivotal importance for the rational design of triptycene-based functional materials, are influenced by noncovalent interactions between substituents mounted on the triptycene skeleton. Herein, a unique interaction between electron-rich substituents in the peri position and the silyl group located on the bridgehead sp3 -carbon is discussed on the example of 1,4-dichloro-9-(p-methoxyphenyl)-silyltriptycene (TRPCl) which exists in solution in the form of two rotamers differing by dispositions, syn or anti, of the Si-CPh (the CPh atom is from the p-methoxyphenyl group) bond against the peri-Cl atom. For the first time, substantial differences between the Si-CPh bonds in these two dispositions are identified, based on indirect experimental and direct theoretical evidence. For these two orientations, the experimental 1 J(Si,CPh ) values differ by as much as 10 percent. The differences are explained in terms of effective electron density transfer from the peri-Cl atom to the antibonding σ* orbitals of the Si-X bonds (X=H, CPh ) oriented anti to that atom. The electronic effects are revealed by an NBO analysis. Connections of these observations with the notion of blue-shifting hydrogen bonds are discussed.
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Affiliation(s)
- Adam Mames
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Banacha 2 C, 02-097, Warsaw, Poland.,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Mariusz Pietrzak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | | | - Sławomir Szymański
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Tomasz Ratajczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
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9
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Casañal A, Lohkamp B, Emsley P. Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data. Protein Sci 2020; 29:1069-1078. [PMID: 31730249 PMCID: PMC7096722 DOI: 10.1002/pro.3791] [Citation(s) in RCA: 334] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022]
Abstract
Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo‐EM model building and refinement, as cryo‐EM structures with resolution ranging 2.5–4 A are now routinely available. Model building into these maps can be time‐consuming and requires experience in both biochemistry and building into low‐resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot. Some examples include morphing, Geman‐McClure restraints, full‐chain refinement, and Fourier‐model based residue‐type‐specific Ramachandran restraints. Here, we present the current state‐of‐the‐art in Coot usage.
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Affiliation(s)
- Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Bernhard Lohkamp
- Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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10
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Sychrovský V, Šaman D, Fiala R, Humpa O, Sýkora J, Kessler P, Blechta V, Dobrev P, Schraml J. Ascorbigen A-NMR identification. Magn Reson Chem 2019; 57:1084-1096. [PMID: 31257662 DOI: 10.1002/mrc.4890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
The connectivities of all atoms in ascorbigen A, an important metabolite, were determined unambiguously for the first time. The connectivity between carbon atoms was established by 2D INADEQUATE, and one-bond 13 C-13 C coupling constants were determined for all pairs of directly connected carbon atoms except for two strongly coupled carbon pairs. The 13 C-13 C coupling in one of the pairs was proved by a modification of standard INADEQUATE; however, the signals from the other pair were too weak to be observed. The connectivity within the two strongly coupled C-C pairs was confirmed by a combination of COSY and gHSQC; the latter experiment also identified all C-H bonds. The proton nuclear magnetic resonance (1 H NMR) spectra in dry dimethyl sulfoxide allowed identification and assignment of the signals due to NH and OH protons. The derived structure, 3-((1H-indol-3-yl)methyl)-3,3a,6-trihydroxytetrahydrofuro[3,2-b]furan-2(5H)-one, agrees with the structure suggested for ascorbigen A in 1966. The density functional theory (DFT) calculations showed that among 16 possible stereoisomers, only two complied with the almost zero value of the measured 3 J(H6-H6a). Of the two stereoisomers, 3S,3aS,6S,6aR and 3R,3aR,6R,6aS, the latter was excluded on synthetic grounds. The nuclear Overhauser effect measurements unveiled close proximity between H2' proton of the indole and the H6a proton of the tetrahydrofuro[3,2-b]furan part. Detailed structural interpretation of the measured NMR parameters by means of DFT NMR was hampered by rotational flexibility of the indole and tetrahydrofuro[3,2-b]furan parts and inadequacy of Polarizable Continuum Model (PCM) solvent model.
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Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czech Republic
| | - David Šaman
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czech Republic
| | | | | | - Jan Sýkora
- Institute of Chemical Process Fundamentals of the CAS, Prague 6, Czech Republic
| | | | - Vratislav Blechta
- Institute of Chemical Process Fundamentals of the CAS, Prague 6, Czech Republic
| | - Petre Dobrev
- Institute of Experimental Botany of the CAS, Prague 6, Czech Republic
| | - Jan Schraml
- Institute of Chemical Process Fundamentals of the CAS, Prague 6, Czech Republic
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11
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Dauzhenka T, Kundrotas PJ, Vakser IA. Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking. J Comput Chem 2018; 39:2012-2021. [PMID: 30226647 DOI: 10.1002/jcc.25381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/24/2018] [Accepted: 05/26/2018] [Indexed: 11/07/2022]
Abstract
Protein-protein docking procedures typically perform the global scan of the proteins relative positions, followed by the local refinement of the putative matches. Because of the size of the search space, the global scan is usually implemented as rigid-body search, using computationally inexpensive intermolecular energy approximations. An adequate refinement has to take into account structural flexibility. Since the refinement performs conformational search of the interacting proteins, it is extremely computationally challenging, given the enormous amount of the internal degrees of freedom. Different approaches limit the search space by restricting the search to the side chains, rotameric states, coarse-grained structure representation, principal normal modes, and so on. Still, even with the approximations, the refinement presents an extreme computational challenge due to the very large number of the remaining degrees of freedom. Given the complexity of the search space, the advantage of the exhaustive search is obvious. The obstacle to such search is computational feasibility. However, the growing computational power of modern computers, especially due to the increasing utilization of Graphics Processing Unit (GPU) with large amount of specialized computing cores, extends the ranges of applicability of the brute-force search methods. This proof-of-concept study demonstrates computational feasibility of an exhaustive search of side-chain conformations in protein pocking. The procedure, implemented on the GPU architecture, was used to generate the optimal conformations in a large representative set of protein-protein complexes. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Taras Dauzhenka
- Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047
| | - Petras J Kundrotas
- Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047
| | - Ilya A Vakser
- Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047.,Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, 66047
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12
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Watkins AM, Craven TW, Renfrew PD, Arora PS, Bonneau R. Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers. Structure 2017; 25:1771-1780.e3. [PMID: 29033287 PMCID: PMC5845441 DOI: 10.1016/j.str.2017.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 06/21/2017] [Accepted: 09/14/2017] [Indexed: 01/28/2023]
Abstract
β-Amino acids offer attractive opportunities to develop biologically active peptidomimetics, either employed alone or in conjunction with natural α-amino acids. Owing to their potential for unique conformational preferences that deviate considerably from α-peptide geometries, β-amino acids greatly expand the possible chemistries and physical properties available to polyamide foldamers. Complete in silico support for designing new molecules incorporating non-natural amino acids typically requires representing their side-chain conformations as sets of discrete rotamers for model refinement and sequence optimization. Such rotamer libraries are key components of several state-of-the-art design frameworks. Here we report the development, incorporation in to the Rosetta macromolecular modeling suite, and validation of rotamer libraries for β3-amino acids.
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Affiliation(s)
- Andrew M Watkins
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Timothy W Craven
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Institute for Protein Design, University of Washington, Seattle, WA 98102, USA
| | - P Douglas Renfrew
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10009, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, NY 10009, USA.
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13
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Riddell IA, Johnstone TC, Park GY, Lippard SJ. Nucleotide Binding Preference of the Monofunctional Platinum Anticancer-Agent Phenanthriplatin. Chemistry 2016; 22:7574-81. [PMID: 27111128 PMCID: PMC4884344 DOI: 10.1002/chem.201600236] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/10/2022]
Abstract
The monofunctional platinum anticancer agent phenanthriplatin generates covalent adducts with the purine bases guanine and adenine. Preferential nucleotide binding was investigated by using a polymerase stop assay and linear DNA amplification with a 163-base pair DNA double helix. Similarly to cisplatin, phenanthriplatin forms the majority of adducts at guanosine residues, but significant differences in both the number and position of platination sites emerge when comparing results for the two complexes. Notably, the monofunctional complex generates a greater number of polymerase-halting lesions at adenosine residues than does cisplatin. Studies with 9-methyladenine reveal that, under abiological conditions, phenanthriplatin binds to the N(1) or N(7) position of 9-methyladenine in approximately equimolar amounts. By contrast, comparable reactions with 9-methylguanine afforded only the N(7) -bound species. Both of the 9-methyladenine linkage isomers (N(1) and N(7) ) exist as two diastereomeric species, arising from hindered rotation of the aromatic ligands about their respective platinum-nitrogen bonds. Eyring analysis of rate constants extracted from variable-temperature NMR spectroscopic data revealed that the activation energies for ligand rotation in the N(1) -bound platinum complex and the N(7) -linkage isomers are comparable. Finally, a kinetic analysis indicated that phenanthriplatin reacts more rapidly, by a factor of eight, with 9-methylguanine than with 9-methyladenine, suggesting that the distribution of lesions formed on double-stranded DNA is kinetically controlled. In addition, implications for the potent anticancer activity of phenanthriplatin are discussed herein.
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Affiliation(s)
- Imogen A Riddell
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
| | - Timothy C Johnstone
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
| | - Ga Young Park
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
| | - Stephen J Lippard
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA.
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14
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Geffe M, Andernach L, Trapp O, Opatz T. Chromatographically separable rotamers of an unhindered amide. Beilstein J Org Chem 2014; 10:701-6. [PMID: 24778722 PMCID: PMC3999880 DOI: 10.3762/bjoc.10.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
Surprisingly stable formamide rotamers were encountered in the tetrahydroisoquinoline and morphinan series of alkaloids. We investigated the hindered rotation around the amide bond by dynamic high-performance liquid chromatography (DHPLC) and kinetic measurements of the interconversion of the rotamers which can readily be separated by HPLC as well as TLC. The experimental results of the different methods were compared to each other as well as to results obtained by DFT calculations.
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Affiliation(s)
- Mario Geffe
- Institut für Organische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Lars Andernach
- Institut für Organische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Oliver Trapp
- Organisch-Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Till Opatz
- Institut für Organische Chemie, Johannes Gutenberg Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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15
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Gou Q, Feng G, Evangelisti L, Vallejo-López M, Spada L, Lesarri A, Cocinero EJ, Caminati W. How water interacts with halogenated anesthetics: the rotational spectrum of isoflurane-water. Chemistry 2014; 20:1980-4. [PMID: 24403206 DOI: 10.1002/chem.201303724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 11/07/2022]
Abstract
The rotational spectra of several isotopologues of the 1:1 complex between the inhaled anesthetic isoflurane and water have been recorded and analyzed by using Fourier transform microwave spectroscopy. The rotational spectrum showed a single rotamer, corresponding to the configuration in which the most stable conformer of isolated isoflurane is linked to the water molecule through an almost linear C-H⋅⋅⋅O weak hydrogen bond. All transitions display a hyperfine structure due to the (35)Cl (or (37)Cl) nuclear quadrupole effects.
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Affiliation(s)
- Qian Gou
- Department of Chemistry, University of Bologna, Via Selmi 2, 40126, Bologna (Italy), Fax: (+39) 0512099456
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16
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Abstract
Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the existence of a general energy function for proteins is by no means guaranteed. Here, we present new insights toward the application of machine learning to the problem of finding a general energy function for protein design. Machine learning requires the definition of an objective function, which carries with it the implied definition of success in protein design. We explored four functions, consisting of two functional forms, each with two criteria for success. Optimization was carried out by a Monte Carlo search through the space of all variable parameters. Cross-validation of the optimized energy function against a test set gave significantly different results depending on the choice of objective function, pointing to relative correctness of the built-in assumptions. Novel energy cross terms correct for the observed nonadditivity of energy terms and an imbalance in the distribution of predicted amino acids. This paper expands on the work presented at the 2012 ACM-BCB.
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17
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Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci 2010; 19:1420-31. [PMID: 20499387 PMCID: PMC2974833 DOI: 10.1002/pro.423] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/04/2010] [Accepted: 05/05/2010] [Indexed: 11/06/2022]
Abstract
Although proteins populate large structural ensembles, X-ray diffraction data are traditionally interpreted using a single model. To search for evidence of alternate conformers, we developed a program, Ringer, which systematically samples electron density around the dihedral angles of protein side chains. In a diverse set of 402 structures, Ringer identified weak, nonrandom electron-density features that suggest of the presence of hidden, lowly populated conformations for >18% of uniquely modeled residues. Although these peaks occur at electron-density levels traditionally regarded as noise, statistically significant (P < 10(-5)) enrichment of peaks at successive rotameric chi angles validates the assignment of these features as unmodeled conformations. Weak electron density corresponding to alternate rotamers also was detected in an accurate electron density map free of model bias. Ringer analysis of the high-resolution structures of free and peptide-bound calmodulin identified shifts in ensembles and connected the alternate conformations to ligand recognition. These results show that the signal in high-resolution electron density maps extends below the traditional 1 sigma cutoff, and crystalline proteins are more polymorphic than current crystallographic models. Ringer provides an objective, systematic method to identify previously undiscovered alternate conformations that can mediate protein folding and function.
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Affiliation(s)
- P Therese Lang
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, California 97420-3220
| | - Ho-Leung Ng
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, California 97420-3220
| | - James S Fraser
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, California 97420-3220
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, California 97420-3220
| | - Nathaniel Echols
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, California 97420-3220
| | - Mark Sales
- Department of Physics, University of CaliforniaBerkeley, California 97420
| | - James M Holton
- Department of Biochemistry and Biophysics, University of CaliforniaSan Francisco, California 94158-2330
- Advanced Light Source, Lawrence Berkeley National LaboratoryBerkeley, California 94720
| | - Tom Alber
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, California 97420-3220
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18
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Unruh JR, Kuczera K, Johnson CK. Conformational heterogeneity of a leucine enkephalin analogue in aqueous solution and sodium dodecyl sulfate micelles: comparison of time-resolved FRET and molecular dynamics simulations. J Phys Chem B 2009; 113:14381-92. [PMID: 19780516 PMCID: PMC2780025 DOI: 10.1021/jp903302k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have undertaken time-resolved Förster resonance energy transfer (FRET) and molecular dynamics simulations to analyze conformations and conformational heterogeneity of an analogue of leucine enkephalin in solution and in the presence of sodium dodecyl sulfate (SDS) micelles. Enkephalins are opioid pentapeptides that interact with opioid receptors in the central nervous system. We used time-correlated single-photon counting to detect energy transfer between the N-terminal tyrosine and a tryptophan residue substituted for phenylalanine at the 4 position. FRET from Tyr to Trp was measured over a temperature range from 5 to 55 degrees C in aqueous solution. By taking into account Tyr rotamer interconversion rates measured previously, we determined average distances between Tyr and Trp for the two populated rotameric conformations of Tyr. Molecular dynamics simulations (100 ns) support this analysis and indicate extensive conformational heterogeneity. The simulations also predict that the FRET orientational factor is correlated with the Tyr-Trp separation. Failure to account for the correlation between orientation and distance results in errors that appear to be largely offset in the leucine enkephalin analogue (YGGWL) by a weighting bias inherent in the R(-6) dependence of the energy-transfer rate. The Tyr lifetimes decrease upon titration of the peptides with SDS, indicating formation of compact conformations of the peptide in the micelle environment. This result is consistent with the conjecture that the lipid environment may induce formation of bioactive conformations of the peptide.
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Affiliation(s)
- Jay R. Unruh
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
| | - Krzysztof Kuczera
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045
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19
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Pendley SS, Yu YB, Cheatham TE. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils. Proteins 2009; 74:612-29. [PMID: 18704948 PMCID: PMC2692595 DOI: 10.1002/prot.22177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The alpha-helical coiled-coil is one of the most common oligomerization motifs found in both native and engineered proteins. To better understand the stability and dynamics of the coiled-coil motifs, including those modified by fluorination, several fluorinated and nonfluorinated parallel dimeric coiled-coil protein structures were designed and modeled. We also attempt to investigate how changing the length and geometry of the important stabilizing salt bridges influences the coiled-coil protein structure. Molecular dynamics (MD) and free energy simulations with AMBER used a particle mesh Ewald treatment of the electrostatics in explicit TIP3P solvent with balanced force field treatments. Preliminary studies with legacy force fields (ff94, ff96, and ff99) show a profound instability of the coiled-coil structures in short MD simulation. Significantly, better behavior is evident with the more balanced ff99SB and ff03 protein force fields. Overall, the results suggest that the coiled-coil structures can readily accommodate the larger acidic arginine or S-2,7-diaminoheptanedoic acid mutants in the salt bridge, whereas substitution of the smaller L-ornithine residue leads to rapid disruption of the coiled-coil structure on the MD simulation time scale. This structural distortion of the secondary structure allows both the formation of large hydration pockets proximal to the charged groups and within the hydrophobic core. Moreover, the increased structural fluctuations and movement lead to a decrease in the water occupancy lifetimes in the hydration pockets. In contrast, analysis of the hydration in the stable dimeric coiled-coils shows high occupancy water sites along the backbone residues with no water occupancy in the hydrophobic core, although transitory water interactions with the salt bridge residues are evident. The simulations of the fluorinated coiled-coils suggest that in some cases fluorination electrostatically stabilizes the intermolecular coiled-coil salt bridges. Structural analyses also reveal different side chain rotamer preferences for leucine when compared with 5,5,5,5',5',5'-hexafluoroleucine mutants. These observed differences in the side chain rotamer populations suggest differential changes in the side chain conformational entropy upon coiled-coil formation when the protein is fluorinated. The free energy of hydration of the isolated 5,5,5,5',5',5'-hexafluoroleucine amino acid is calculated to be 1.1 kcal/mol less stable than leucine; this hydrophobic penalty in the monomer may provide a driving force for coiled-coil dimer formation. Estimation of the ellipticity at 222 nm from a series of snapshots from the MD simulations with DicroCalc shows distinct increases in the ellipticity when the coiled-coil is fluorinated, which suggests that the helicity in the folded coiled-coils is greater when fluorinated.
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Affiliation(s)
- Scott S. Pendley
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| | - Yihua B. Yu
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Departments of Pharmaceutical Sciences and Bioengineering, University of Maryland, University of Maryland, 20 Penn Street, Rm. 635, Baltimore, MD 21201
| | - Thomas E. Cheatham
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Medicinal Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Bioengineering, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
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20
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Abstract
Protein-protein interactions are the key to many biological processes. How proteins selectively and correctly associate with their required protein partner(s) is still unclear. Previous studies of this "protein-docking problem" have found that shape complementarity is a major determinant of interaction, but the detailed balance of energy contributions to association remains unclear. This study estimates side-chain conformational entropy (per unit solvent accessible area) for various protein surface regions, using a self-consistent mean field calculation of rotamer probabilities. Interfacial surface regions were less flexible than the rest of the protein surface for calculations with monomers extracted from homodimer datasets in 21 of 25 cases, and in 8 of 9 for the large protomer from heterodimer datasets. In surface patch analysis, based on side-chain conformational entropy, 68% of true interfaces were ranked top for the homodimer set and 66% for the large protomer/heterodimer set. The results indicate that addition of a side-chain entropic term could significantly improve empirical calculations of protein-protein association.
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Affiliation(s)
- Christian Cole
- Department of Biomolecular Sciences, UMIST, Manchester M60 1QD, UK
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21
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Shortle D. Composites of local structure propensities: evidence for local encoding of long-range structure. Protein Sci 2002; 11:18-26. [PMID: 11742118 PMCID: PMC2368770 DOI: 10.1110/ps.ps.31002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2001] [Revised: 10/01/2001] [Accepted: 10/04/2001] [Indexed: 10/16/2022]
Abstract
To estimate how extensively the ensemble of denatured-state conformations is constrained by local side-chain-backbone interactions, propensities of each of the 20 amino acids to occur in mono- and dipeptides mapped to discrete regions of the Ramachandran map are computed from proteins of known structure. In addition, propensities are computed for the trans, gauche-, and gauche+ rotamers, with or without consideration of the values of phi and psi. These propensities are used in scoring functions for fragment threading, which estimates the energetic favorability of fragments of protein sequence to adopt the native conformation as opposed to hundreds of thousands of incorrect conformations. As finer subdivisions of the Ramachandran plot, neighboring residue phi/psi angles, and rotamers are incorporated, scoring functions become better at ranking the native conformation as the most favorable. With the best composite propensity function, the native structure can be distinguished from 300,000 incorrect structures for 71% of the 2130 arbitrary protein segments of length 40, 48% of 2247 segments of length 30, and 20% of 2368 segments of length 20. A majority of fragments of length 30-40 are estimated to be folded into the native conformation a substantial fraction of the time. These data suggest that the variations observed in amino acid frequencies in different phi/psi/chi1 environments in folded proteins reflect energetically important local side-chain-backbone interactions, interactions that may severely restrict the ensemble of conformations populated in the denatured state to a relatively small subset with nativelike structure.
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Affiliation(s)
- David Shortle
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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