Structure determination biopolymers

Many of the same models and techniques have been used to study the transitions in these two types of biopolymers, and we will present some common background information first. Then we will specialize and present the results of important thermodynamic studies in proteins and nucleic acids separately. However, common to both reports is the observation that the application of thermodynamic measurements and a thermodynamic analysis to carefully but widely chosen systems allows one to gain insights into structural details that complement molecular structure determinations obtained from instrumental techniques such as spectroscopy and X-ray crystallography. 

The structure determination of biopolymers using NMR spectroscopy usually involves interactions of protons[25,1221. Typically, interactions of protons (nuclear Over-... 

This collection of papers was part of a unique symposium held during the 178th Meeting of the American Chemical Society. The symposium, Diffraction Methods for Structural Determination of Fibrous Polymers, had a pronounced international character, with scientists from 12 different countries. The speakers represented both the synthetic polymer and biopolymer fields, with contributions in each of the three classes of natural polymers nucleic acids, proteins, and polysaccharides. Most important, the symposium centered on methods and techniques for studying fibrous polymers, methods that are usually taken for granted despite their inadequacies. 

The main source of conformational information for biopolymers are the easy-to-obtain chemical shifts that can be translated into dihedral restraints. In addition, for fully 13C labeled compounds, proton-driven spin diffusion between carbons [72] can be used to measure quantitatively distances between carbons. The CHHC experiment is the equivalent of the NOESY in solution that measures distances between protons by detecting the resonances of the attached carbons. While both techniques, proton-driven spin diffusion and CHHC experiment [73], allow for some variation in the distance as determined from cross-peak integrals, REDOR [74] experiments in selective labeled compounds measure very accurate distances by direct observation of the oscillation of a signal by the dipolar coupling. While the latter technique provides very accurate distances, it provides only one piece of information per sample. Therefore, the more powerful techniques proton-driven spin diffusion and CHHC have taken over when it comes to structure determination by ss-NMR of fully labeled ligands. 

The structure determination of biopolymers using NMR spectroscopy usually involves interactions of protons[216,33. Typically, interactions of protons (nuclear Overhauser effect, NOE) that are close in space but separated by several subunits of the biopolymer are used to establish the folding of the backbone. Distance restraints are then used to compute a structure which is checked by back-calculation of the NOE spectra and comparison with experimental results 361. For large and highly flexible systems molecular dynamics is invaluable for scanning the conformational space. 

The Encyclopedia of NMR1 contains a very large number of articles on biological applications of NMR, including discussions of the methodology used for three-dimensional structure determination, along with presentations on individual biopolymers. 

R595 H. Zhou, A. Vermeulen, F. M. Jucker and A. Pardi, Incorporating Residual Dipolar Couplings into the NMR Solution Structure Determination of Nucleic Acids , Biopolymers, 1999-2000, 52, 168... 

These interactions are frequently ionic in character. The coulombic forces of interaction between macroions and lower molecular weight ionic species are central to the life processes of the cell. For example, intermolecular interactions of nucleic acids with proteins and small ions, of proteins with anionic lipids and surfactants and with the ionic substrates of enzyme catalyzed reactions, and of ionic polysaccharides with a variety of inorganic cations are all improtant natural processes. Intramolecular coulombic interactions are also important for determining the shape and stability of biopolymer structures, the biological function of which frequently depends intimately on the conformational features of the molecule. 

The experimental studies on biopolymer structures are increasingly supplemented by computational approaches. First, it has to be realized that computation is a sine qua non for experimental structure determination by diffraction methods and NMR spectroscopy themselves. In addition, independent computational studies can provide useful information on structure and dynamics of biopolymers not accessible, at least currently, by experiments. With regard to base poiyads there are three fields that have to be mentioned here primarily quantum-chemical studies of nucleic building blocks, MD simulations of medium-sized nucleic acids and structural bioinformatics. 

Quadrupole ion traps ions are dynamically stored in a three-dimensional quadrupole ion storage device (Fig. 10.6) [37]. The RF and DC potentials can be scanned to eject successive mass-to-charge ratios from the trap into the detector (mass-selective ejection). Ions are formed within the ion trap or injected into an ion trap from an external source. The ions are dynamically trapped by the applied RF potentials (a common trap design also makes use of a bath gas to help contain the ions in the trap). The trapped ions can be manipulated by RF events to perform ion ejection, ion excitation, and mass-selective ejection. This provides MS/MS and MS experiments, which are eminently suited for structure determinations of biopolymers [38] (see Section 10.4). 

The measurement and interpretation of RDCs between spatially proximate spin-pairs in biopolymers such as proteins, nucleic acids, and oligosaccharides in partially oriented environments has become a popular method for structure determination." All observed RDCs, D s contain an unknown contribution from the anisotropic part of coupling tensor, J in addition to the direct dipolar contribution, Bryce and Wasylishen" evaluated the influence of J on RDCs... 

Burchard W. Static and dynamic light scattering approaches to structure determination in biopolymers. In Harding SE, Sattelle DB, Bloomfield VA, editors. Laser Light Scattering in Biochemistry. Cambridge, UK Royal Society Chemistry 1992. p 3-22. 

For structural determination of biopolymers, multidimensional (three or more) NMR spectroscopy is helpful, as the spectrum carries a number of... 

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