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Russo L, Raiola L, Campitiello MA, Magrì A, Fattorusso R, Malgieri G, Pappalardo G, La Mendola D, Isernia C. Probing the residual structure in avian prion hexarepeats by CD, NMR and MD techniques. Molecules 2013; 18:11467-84. [PMID: 24043142 PMCID: PMC6270093 DOI: 10.3390/molecules180911467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 02/06/2023] Open
Abstract
Many proteins perform essential biological functions by means of regions that lacking specific organized structure exist as an ensemble of interconverting transient conformers. The characterization of such regions, including the description of their structural propensities, number of conformations and relative populations can provide useful insights. Prion diseases result from the conversion of a normal glycoprotein into a misfolded pathogenic isoform. The structures of mammal and chicken prion proteins show a similar fold with a globular domain and a flexible N-terminal portion that contains different repeated regions: octarepeats (PHGGGWGQ) in mammals and hexarepeats (PHNPGY) in chickens. The higher number of prolines in the hexarepeat region suggests that this region may retain a significant amount of residual secondary structure. Here, we report the CD, NMR and MD characterization of a peptide (2-HexaPY) composed of two hexarepeats. We combine experimental NMR data and MD to investigate at atomic level its ensemble-averaged structural properties, demonstrating how each residue of both repeats has a different quantified PPII propensity that shows a periodicity along the sequence. This feature explains the absence of cooperativity to stabilize a PPII conformation. Nonetheless, such residual structure can play a role in nucleating local structural transitions as well as modulating intra-molecular or inter-molecular interactions.
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Affiliation(s)
- Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Luca Raiola
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Maria Anna Campitiello
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Antonio Magrì
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Giuseppe Pappalardo
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy; E-Mail:
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-0823-274-636; Fax: +39-0823-274-605
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Ward RA, Kettle JG. Systematic Enumeration of Heteroaromatic Ring Systems as Reagents for Use in Medicinal Chemistry. J Med Chem 2011; 54:4670-7. [DOI: 10.1021/jm200338a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard A. Ward
- Oncology iMED, AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Jason G. Kettle
- Oncology iMED, AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
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Martín EI, Martínez JM, Sánchez Marcos E. Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine. J Chem Phys 2011; 134:024503. [PMID: 21241116 DOI: 10.1063/1.3528934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.
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Affiliation(s)
- Elisa I Martín
- Departamento de Química Física, Universidad de Sevilla, E-41012 Sevilla, Spain
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Abstract
We apply recently developed techniques for pattern recognition to construct a generative model for chemical structure. This approach can be viewed as ligand-based de novo design. We construct a statistical model describing the structural variations present in a set of molecules which may be sampled to generate new structurally similar examples. We prevent the possibility of generating chemically invalid molecules, according to our implicit hydrogen model, by projecting samples onto the nearest chemically valid molecule. By populating the input set with molecules that are active against a target, we show how new molecules may be generated that will likely also be active against the target.
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Affiliation(s)
- David White
- Software Technologies Research Group, University of Bamberg, 96047 Bamberg, Germany
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Kutchukian PS, Lou D, Shakhnovich EI. FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space. J Chem Inf Model 2009; 49:1630-42. [DOI: 10.1021/ci9000458] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Peter S. Kutchukian
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - David Lou
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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Zikic R, Krstić PS, Zhang XG, Fuentes-Cabrera M, Wells J, Zhao X. Characterization of the tunneling conductance across DNA bases. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:011919. [PMID: 16907139 DOI: 10.1103/physreve.74.011919] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Indexed: 05/11/2023]
Abstract
Characterization of the electrical properties of the DNA bases (adenine, cytosine, guanine, and thymine), in addition to building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotidelike molecules of the DNA bases, placed in a 1.5 nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the density-functional theory exchange-correlation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.
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Affiliation(s)
- Radomir Zikic
- Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, USA
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Bohacek RS, McMartin C. Modern computational chemistry and drug discovery: structure generating programs. Curr Opin Chem Biol 1997; 1:157-61. [PMID: 9667851 DOI: 10.1016/s1367-5931(97)80004-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During 1996 and 1997, the first reports were disclosed of active enzyme inhibitors based entirely on novel structures created by de novo methods. De novo methods have also been used to modify and significantly improve the binding affinity of an HIV protease inhibitor. Work continues in the improvement of methods for the de novo design of compounds which fit and chemically complement a binding site. De novo algorithms that generate only synthetically feasible structures have also been reported. In addition, methods are being developed for the automatic computer generation of virtual molecular libraries which can be searched to identify molecules to match a pharmacophore or fit into a binding site.
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Affiliation(s)
- R S Bohacek
- ARIAD Pharmaceuticals, Inc., 26 Landsdowne Street, Cambridge, MA 02139, USA
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