Recently proposed self-consistent 3J coupling analysis (Schmidt, J. M.; Blümel, M.; Löhr, F.; Rüterjans, H. J. Biomol. NMR 1999, 14, 1-12) has been carried out to calibrate Karplus parameters constituting the empirical dependence of 3J coupling constants on the chi1 dihedral angle in amino acid side chains. The procedure involves simultaneous least-squares optimization of six sets of three Karplus coefficients related to all six 3J coupling types accessible in 15N,13C-labeled proteins. A simple concept of fundamental and incremental component couplings is proposed to account for substituent effects, eventually yielding amino acid topology-specific Karplus parameters. The method is exemplified with recombinant Desulfovibrio vulgaris flavodoxin (147 amino acids, 16 kDa) with reference to a total of 749 experimental 3JHalpha,Hbeta, 3JN',Hbeta, 3JC',Hbeta, 3JHalpha,Cgamma, 3JN',Cgamma, and 3JC',Cgamma coupling constants. Unlike other parametrizations, the present method does not make reference to X-ray coordinates, so that the Karplus coefficients obtained are not influenced by differences between solution and crystal states. Cross validation using X-ray torsion angles demonstrates the improvement relative to previous parametrizations. The Karplus coefficients derived are applicable to other proteins, too. Parameter refinement also yields a series of chi1 torsion angles, providing valuable constraints for protein structure determination, as well as optional parameters of local angular mobility in the contexts of Gaussian random fluctuation or a three-site jump model. The procedure permits automatic stereospecific assignments of Hbeta and Cgamma chemical shifts. The majority of the flavodoxin side-chain conformations agrees with high-resolution X-ray structures of the protein. Marked deviations between NMR and X-ray datasets are attributed to different rotameric states due to crystal-packing effects and to conformational equilibria between multiple chi1 rotamers.

Treatment of patients with chronic hepatitis C with recombinant interferon alfa (rIFN-␣) can achieve clearance of the hepatitis C virus (HCV) from serum and liver. However, the overall sustained virological response to IFN-␣ monotherapy is less than 20%. 1,2 Additional clinical trials have been conducted to evaluate alternative treatment modalities in chronic hepatitis C, including therapy with ribavirin. While ribavirin monotherapy revealed no consistent effect on HCV RNA relative to placebo, 3,4 results of combination therapy with subcutaneously administered rIFN-␣ and orally administered ribavirin suggested a potential synergistic effect. [5][6][7] Ribavirin (1-␤-D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide) is a synthetic purine nucleoside that is structurally similar to guanosine. The drug rapidly enters eukaryotic cells, and after intracellular phosphorylation exhibits virustatic activity against a broad spectrum of DNA and RNA viruses. Several possible mechanisms of action have been proposed, including depletion of the intracellular guanosine triphosphate pools, synthesis of RNA with abnormal 5Јcap structures, and inhibition of viral polymerase activity. Furthermore, ribavirin has detectable effects on host immune responses. The detailed mechanism of action, however, is unknown. 4,8 In the present study, we treated patients chronically infected with HCV with either 3 ϫ 3 MU rIFN-␣ per week, 3 ϫ 6 MU rIFN-␣ per week, or 3 ϫ 6 MU rIFN-␣ per week plus 14 mg/kg of body weight ribavirin per day to perturb the balance between virus production and clearance. From serial measurements of changes in viremia in patients responding to antiviral therapy, we obtained kinetic information on the dynamics of HCV replication in vivo. Numerical data modeling was performed to compare the direct antiviral efficacy of the three different treatment schedules. PATIENTS AND METHODSIn this study, 26 patients chronically infected with HCV were treated with 3 MU rIFN-␣ three times per week subcutaneously. In a different cohort of 37 patients, we administered 6 MU rIFN-␣ three times per week subcutaneously. Eighteen patients of this cohort were randomized to receive ribavirin (14 mg per kg of body weight, i.e., 900-1,200 mg) in two divided doses orally per day. Duration of treatment is scheduled for 12 months; the trials are ongoing. All patients were previously untreated, and the diagnosis of chronic hepatitis C was based on elevated serum transaminase levels, histological examination, and the consistent detection of anti-HCV antibodies (third-generation assay) and HCV RNA. All patients were hepatitis B surface antigen-negative and negative for the antibody to the human immunodeficiency virus type 1 and type 2. Blood samples were obtained 4 and 1 week before initiation of treatment and subsequently at days 0, 1, 3, 7, 14, 21, 28, and 56. Serum was prepared under a laminar flow bench and frozen at Ϫ80°C. Serum HCV RNA levels were quantified as recently described in detail. [9][10][11] Abbreviations: rIFN-␣, recombinant interferon ...

A general procedure for the analysis of biomolecular structures by NMR in the presence of rapid conformational dynamics has been applied to the study of the cyclic decapeptide antamanide. Two-dimensional experiments, relaxation measurements in the rotating frame, and homo- and heteronuclear coupling constant determinations have been used to characterize the dynamic properties of the molecule, in combination with a novel search algorithm for investigating multiconformational equilibria. Direct evidence for the presence of a conformational exchange process with an activation energy of approximately 20 kJ mol-1 and an exchange lifetime of approximately 25 microseconds at 320 K has been obtained from rotating frame relaxation measurements. This evidence is combined with the information derived from the multiconformational search algorithm MEDUSA to propose sets of structures that coexist in a dynamic exchange equilibrium.

The concept of self-consistent J coupling evaluation exploits redundant structure information inherent in large sets of 3J coupling constants. Application to the protein Desulfovibrio vulgaris flavodoxin demonstrates the simultaneous refinement of torsion-angle values and related Karplus coefficients. The experimental basis includes quantitative coupling constants related to the polypeptide backbone φ torsion originating from a variety of heteronuclear 2D and 3D NMR correlation experiments, totalling 124 3J(HN,Hα), 129 3J(HN,C'), 121 3J(HN,Cβ), 128 3J(C'i-1,Hαi), 121 3J(C'i-1,C'i), and 122 3J(C'i-1,Cβi). Without prior knowledge from either X-ray crystallography or NMR data, such as NOE distance constraints, accurate φ dihedral angles are specified for 122 non-glycine and non-proline residues out of a total of 147 amino acids. Different models of molecular internal mobility are considered. The Karplus coefficients obtained are applicable to the conformational analysis of φ torsions in other polypeptides.