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Full-Text Articles in Physical Sciences and Mathematics
Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer
Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer
Chemistry Faculty Publications
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of > 80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg2+ rigidifies Loop E and stabilizes its major groove at an intermediate …
Tools For The Automatic Identification And Classification Of Rna Base Pairs, Neocles B. Leontis, Huanwang Yang, Fabrice Jossinet, Li Chen, John Westbrook, Helen Berman, Eric Westhof
Tools For The Automatic Identification And Classification Of Rna Base Pairs, Neocles B. Leontis, Huanwang Yang, Fabrice Jossinet, Li Chen, John Westbrook, Helen Berman, Eric Westhof
Chemistry Faculty Publications
Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate …
Peptide-Protein Interactions: Photoinduced Electron-Transfer Within The Preformed And Encounter Complexes Of A Designed Metallopeptide And Cytochrome C, Robin C. Lasey, Liu Liu, Ling Zang, Michael Y. Ogawa
Peptide-Protein Interactions: Photoinduced Electron-Transfer Within The Preformed And Encounter Complexes Of A Designed Metallopeptide And Cytochrome C, Robin C. Lasey, Liu Liu, Ling Zang, Michael Y. Ogawa
Chemistry Faculty Publications
Photoinduced electron-transfer (ET) occurs between a negatively charged metallopeptide, [Ru(bpy)2(phen-am)-Cys-(Glu)(5)-Gly](3-) = RuCE(5)G, and ferricytochrome c = Cyt c. In the presence of Cyt c, the triplet state lifetime of the ruthenium metallopeptide is shortened, and the emission decays via biexponential kinetics, which indicates the existence of two excited-state populations of ruthenium peptides. The faster decay component displays concentration-independent kinetics demonstrating the presence of a preformed peptide-protein complex that undergoes intra-complex electron-transfer. Values of K-b = (3.5 +/- 0.2) x 10(4) M-1 and k(ET)(obs) = (2.7 +/- 0.4) x 10(6) s(-1) were observed at ambient temperatures. The magnitude of k(ET)(obs) decreases …
Photoinduced Electron-Transfer Along Alpha-Helical And Coiled-Coil Metallopeptides, Anna Fedorova, Anita Chaudhari, Michael Y. Ogawa
Photoinduced Electron-Transfer Along Alpha-Helical And Coiled-Coil Metallopeptides, Anna Fedorova, Anita Chaudhari, Michael Y. Ogawa
Chemistry Faculty Publications
A peptide-based electron-transfer system has been designed in which the specific positions of redox-active metal complexes appended to either an a-helix, or an a-helical coiled-coil, can be reversed to test the effect of the helix dipole in controlling photoinduced electron-transfer rates. Two 30-residue apopeptides were prepared having the following sequences: (1) Ac-K-(IEALEGK)(ICALEGK)(IEALEHK)-(IEALEGK)-G-amide, and (II) Ac-K-(IEALEGK)(IHALEGK)-(IEALECK)(IEALEGK)-G-amide. Each apopeptide was reacted first with [Ru(bpy)(2)(phen-ClAc)](2+), where bpy = 2,2'-bipyridine and phen-ClAc = 5-chloroacetamido-1,10-phenanthroline, to attach the ruthenium polypyridyl center to the cysteine side-chain of the polypeptide. The isolated products were then reacted with [Ru(NH3)(5)(H2O)](2+) to yield the binuclear electron-transfer metallopeptides ET-I and ET-II. …
Self-Aggregates Of Cationic Meso-Tetratolylporphyrins In Aqueous Solutions, Pavel Kubat, Kamil Lang, Kristina Prochazkova, Pavel Anzenbacher Jr.
Self-Aggregates Of Cationic Meso-Tetratolylporphyrins In Aqueous Solutions, Pavel Kubat, Kamil Lang, Kristina Prochazkova, Pavel Anzenbacher Jr.
Chemistry Faculty Publications
Aggregation properties of meso-tetratolylporphyrins bearing cationic substituents of a lipophilic nature such as ammonium, pyridinium, phosphonium, sulfonium, and isothiouronium were studied by UV/vis and resonance light scattering spectroscopy. The exciton point-dipole approximation was used to predict the structural alignment of the porphyrin units within the aggregate. The contribution of various types of aggregates depends on the porphyrin substitution, ionic strength, and temperature of aqueous solution of the porphyrin. In general, the preferred structure of an aggregate formed by temperature-induced aggregation is the J-aggregate exhibiting the characteristically narrow, red-shifted Soret band indicating a parallel "side-by-side" arrangement of the porphyrin units. The …