Observation of Through-Hydrogen-Bond 2hJHC′ in a Perdeuterated Protein
Institute of Structural Biology, Forschungszentrum Jülich, Jülich, 52425, Germany. Journal of Magnetic Resonance
(Impact Factor: 2.51).
11/1999; 140(2):510-2. DOI: 10.1006/jmre.1999.1899
It is demonstrated that J connectivity between amide protons and hydrogen-bond-accepting carbonyl carbons can be observed in perdeuterated human ubiquitin. A selective pulse scheme is used to detect these small 2hJHC' interactions in the presence of the much larger through-covalent-bond 2JHC' and 3JHC' couplings. The ratio of the observed through-H-bond correlation intensity and the 2JHC' connectivity observed in a reference spectrum indicates 2hJHC' values of ca. 0.4-0.6 Hz, which are only slightly smaller than the corresponding 3hJNC' values. However, for technical reasons, 2hJHC' couplings are more difficult to measure than 3hJNC'.
Available from: Ramgopal R Mettu
- "NMR chemical shifts (Marin et al., 2004; Wishart and Sykes, 1994; Wishart et al., 1991, 1992) or automated assignment (Bailey-Kellogg et al., 2000a) can also be used. Hydrogen bonds can be determined by NMR from experimentally recorded data (Cordier et al., 1999; Wang et al., 1999), or, e.g., by using backbone resonance assignment programs such as Jigsaw (Bailey-Kellogg et al., 2000a). The user of our algorithm has a choice, to record either (a) one type of backbone RDC (such as NH RDCs) in two aligning media, or (b) two types of backbone RDCs (such as NH and CH RDCs) in a single medium. "
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ABSTRACT: We describe an efficient algorithm for protein backbone structure determination from solution Nuclear Magnetic Resonance (NMR) data. A key feature of our algorithm is that it finds the conformation and orientation of secondary structure elements as well as the global fold in polynomial time. This is the first polynomial-time algorithm for de novo high-resolution biomacromolecular structure determination using experimentally recorded data from either NMR spectroscopy or X-ray crystallography. Previous algorithmic formulations of this problem focused on using local distance restraints from NMR (e.g., nuclear Overhauser effect [NOE] restraints) to determine protein structure. This approach has been shown to be NP-hard, essentially due to the local nature of the constraints. In practice, approaches such as molecular dynamics and simulated annealing, which lack both combinatorial precision and guarantees on running time and solution quality, are used routinely for structure determination. We show that residual dipolar coupling (RDC) data, which gives global restraints on the orientation of internuclear bond vectors, can be used in conjunction with very sparse NOE data to obtain a polynomial-time algorithm for structure determination. Furthermore, an implementation of our algorithm has been applied to six different real biological NMR data sets recorded for three proteins. Our algorithm is combinatorially precise, polynomialtime, and uses much less NMR data to produce results that are as good or better than previous approaches in terms of accuracy of the computed structure as well as running time.
Journal of Computational Biology 10/2006; 13(7):1267-88. DOI:10.1089/cmb.2006.13.1267 · 1.74 Impact Factor
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ABSTRACT: The hydrogen bond H-bond has been recognized in science for more than 80 years as a concept to explain situations where a hydrogen atom is simultaneously binding to two other atoms. Due to the moderate energies necessary for their formation and rupture, hydrogen bonds play a fundamental role in many chemical reactions and most, if not all, interactions involving biological macromolecules. For both proteins and nucleic acids, H-bonds are the essential element in the formation of secondary structures and often they also participate in the stabilization of tertiary structures. Many properties of H-bonds have been studied by a large variety of experimental methods, including NMR spectroscopy. Recently, electron-mediated scalar couplings have been observed which connect magnetic nuclei on both sides of the hydrogen bridge. In contrast to earlier NMR observables, these couplings can be used to ''see'' all partners of the hydrogen bond, the donor, the proton, and the acceptor in a single COSY experiment. In addition, the size of the coupling constant can be related to hydrogen bond distances and angles. This article should serve as an introduction to these findings and illustrate their use by various examples. 2001 John
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ABSTRACT: We describe the first direct observation of NH···OC hydrogen bonding in nucleic acids via the four-bond 4hJNiNj coupling within an N1iH1i···O6jC6j−N1j segment of a G·G·G·G tetrad. The experiment, two-dimensional (2D) HN(N)-TOCSY, makes use of band-selective 15N isotropic mixing to transfer magnetization exclusively via the 4hJNN couplings to yield correlations between N1Hi(ω2) and N1j(ω1) across the hydrogen-bonded segment. In a complementary experiment, 2D cross-polarization (CP)-H(N)CO−(NN)-TOCSY, employing band-selective heteronuclear 15N−13C cross-polarization sequences on either side of the 15N−15N TOCSY period, correlations are obtained between N1Hi(ω2) and C6j(ω1) nuclei across the hydrogen bond. The symmetric A2X2-type coupling topology of the four−spin nitrogen system in the G·G·G·G tetrad permits accurate measurement of these couplings by a new procedure that fits the experimental data with known analytical isotropic mixing transfer functions. The techniques are demonstrated on a G·G·G·G tetrad formed within a novel dimeric quadruplex fold of a uniformly 13C/15N-labeled d(G-G-G-T-T-C-A-G-G) DNA sequence. The value of the 4hJNN coupling constant for this system is estimated to be 0.136 ± 0.021 Hz.
Journal of the American Chemical Society 04/2000; 122(13):3206-3210. DOI:10.1021/ja994255s · 12.11 Impact Factor
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