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Acceptor Distance (acceptor + distance)
Selected AbstractsHydrogen bonding strength,measures based on geometric and topological parameters,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2004awomir Janusz Grabowski Abstract Different methods of estimating H-bond strength are presented. The studies are based on the results of MP2/6,311++G** calculations and the binding energies are corrected for the basis set superposition error (BSSE). The wavefunctions were further applied to localize bond critical points and ring critical points. The characteristics based on the Bader theory are also applied as indicators and measures of hydrogen bonding. This study compares samples of different compounds. The H-bond strength measures such as the proton,acceptor distance (H···Y), the length of the proton donating bond, the electron density at H···Y bond critical point, the H-bond energy and others are analysed. The case of the intramolecular hydrogen bonding is also analysed, and its special characteristics are given. Copyright © 2003 John Wiley & Sons, Ltd. [source] Sequence, Structure and Energy Transfer in DNA,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 3 2007Thomas M. Nordlund Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2-aminopurine (2AP) as an energy trap in short (3- to 20-base) single- and double-stranded DNA oligomers is reviewed. Variation of 2AP's neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3, end, (3) approximate equality of efficiencies for 3, to 5, and 5, to 3, directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de-excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross-strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below ,60°C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single-stranded DNA, are separated by less than 5 Å (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor,acceptor distance, the experimental dependence clearly disagrees with Förster 1/r6 dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base,base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular "fiber optic" face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this "fiber optic" a challenge. [source] An experimental study of GFP-based FRET, with application to intrinsically unstructured proteinsPROTEIN SCIENCE, Issue 7 2007Tomoo Ohashi Abstract We have experimentally studied the fluorescence resonance energy transfer (FRET) between green fluorescent protein (GFP) molecules by inserting folded or intrinsically unstructured proteins between CyPet and Ypet. We discovered that most of the enhanced FRET signal previously reported for this pair was due to enhanced dimerization, so we engineered a monomerizing mutation into each. An insert containing a single fibronectin type III domain (3.7 nm end-to-end) gave a moderate FRET signal while a two-domain insert (7.0 nm) gave no FRET. We then tested unstructured proteins of various lengths, including the charged-plus-PQ domain of ZipA, the tail domain of ,-adducin, and the C-terminal tail domain of FtsZ. The structures of these FRET constructs were also studied by electron microscopy and sedimentation. A 12 amino acid linker and the N-terminal 33 amino acids of the charged domain of the ZipA gave strong FRET signals. The C-terminal 33 amino acids of the PQ domain of the ZipA and several unstructured proteins with 66,68 amino acids gave moderate FRET signals. The 150 amino acid charged-plus-PQ construct gave a barely detectable FRET signal. FRET efficiency was calculated from the decreased donor emission to estimate the distance between donor and acceptor. The donor,acceptor distance varied for unstructured inserts of the same length, suggesting that they had variable stiffness (persistence length). We conclude that GFP-based FRET can be useful for studying intrinsically unstructured proteins, and we present a range of calibrated protein inserts to experimentally determine the distances that can be studied. [source] Conformations within soluble oligomers and insoluble aggregates revealed by resonance energy transferBIOPOLYMERS, Issue 4 2010Jyothi L. Digambaranath Abstract A fluorescently labeled 20-residue polyglutamic acid (polyE) peptide 20 amino acid length polyglutamic acid (E20) was used to study structural changes which occur in E20 as it co-aggregates with other unlabeled polyE peptides. Resonance energy transfer (RET) was performed using an o -aminobenzamide donor at the N-terminus and 3-nitrotyrosine acceptor at the C-terminus of E20. PolyE aggregates were not defined as amyloid, as they were nonfibrillar and did not bind congo red. Circular dichroism measurements indicate that polyE aggregation involves a transition from ,-helical monomers to aggregated ,-sheets. Soluble oligomers are also produced along with aggregates in the reaction, as determined through size exclusion chromatography. Time-resolved and steady-state RET measurements reveal four dominant E20 conformations: (1) a partially collapsed conformation (24 Å donor,acceptor distance) in monomers, (2) an extended conformation in soluble oligomers (>29 Å donor,acceptor distance), (3) a minor partially collapsed conformation (22 Å donor-acceptor distance) in aggregates, and (4) a major highly collapsed conformation (13 Å donor,acceptor distance) in aggregates. These findings demonstrate the use of RET as a means of determining angstrom-level structural details of soluble oligomer and aggregated states of proteins. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 299,317, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Structures of 1-hydrophenanthroimidazoles: building blocks in the synthesis of expanded-ring bis(imidazoles)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Robert T. Stibrany The structures of 1H -phenanthro[9,10- d]imidazole, C15H10N2, (I), and 3,6-dibromo-1H -phenanthro[9,10- d]imidazole hemihydrate, C15H8Br2N2·0.5H2O, (II), contain hydrogen-bonded polymeric chains linked by columns of ,,, stacked essentially planar phenanthroimidazole monomers. In the structure of (I), the asymmetric unit consists of two independent molecules, denoted (Ia) and (Ib), of 1H -phenanthro[9,10- d]imidazole. Alternating molecules of (Ia) and (Ib), canted by 79.07,(3)°, form hydrogen-bonded zigzag polymer chains along the a -cell direction. The chains are linked by ,,, stacking of molecules of (Ia) and (Ib) along the b -cell direction. In the structure of (II), the asymmetric unit consists of two independent molecules of 3,6-dibromo-1H -phenanthro[9,10- d]imidazole, denoted (IIa) and (IIb), along with a molecule of water. Alternating molecules of (IIa), (IIb) and water form hydrogen-bonded polymer chains along the [110] direction. The donor,acceptor distances in these N(imine)...H,O(water)...H,N(amine) hydrogen bonds are the shortest thus far reported for imidazole amine and imine hydrogen-bond interactions with water. Centrosymmetrically related molecules of (IIa) and (IIb) alternate in columns along the a -cell direction and are canted by 48.27,(3)°. The present study provides the first examples of structurally characterized 1H -phenanthroimidazoles. [source] | ||||||||||