Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations

A systematic comparison is made between experimental and computational data gained on vicinal disulfide bridges in proteins and peptides. Structural and stability data of ab initio and density functional theory (DFT) calculations on the model compound 4,5-ditiaheptano-7-lactam and the model peptide HCO-ox-[Cys-Cys]-NH2 at RHF/3-21G*, B3LYP/6-31+G(d), and B3LYP/6-311++G(d,p) levels of theory are presented. The data on Xxx-Cys-Cys-Yyy type amino acid sequence units retrieved from PDB SELECT, along with data on sequence units that have vicinal disulfide bridge, taken from the Brookhaven Protein Data Bank, are conformationally characterized. Amino acid backbone conformations, cis-trans isomerism of the amide bond between the two cysteine residues, and ring puckering are studied. Ring puckers are characterized by their relation to the conformers of the parent 4,5-ditiaheptano-7-lactam. Computational precision and accuracy are proved by frequency calculation and solvent model optimization on selected conformers. It is found that the ox-[Cys-Cys] unit is able to accept types I, II, VIa, VIb, and VIII beta-turn structures.     

Hunting for alternative disulfide bond formation pathways: endoplasmic reticulum janitor turns professor and teaches a lesson

In this issue of Molecular Cell, Ron and colleagues (Zito et al., 2010b) show that an enzyme responsible for cleaning up hydrogen peroxide in the endoplasmic reticulum can contribute productively to disulfide bond formation.     

Protector turns predator

Therapy-induced autophagy is recognized as a critical determinant of treatment outcome in cancer patients, primarily as a factor underlying drug resistance. However, recent investigations point toward a context-dependent, death-inducing role for autophagy, the mechanism of which remains largely unknown. Our recent study provides evidence that autophagy can directly mediate cell killing in multiple tumor cell types by facilitating degradation of KRAS/K-Ras, a key survival protein. These findings have broad implications for strategies employing autophagy modulation to target tumor cells.     

Vicinal coupling constants and protein dynamics

The effects of motional averaging on the analysis of vicinal spin-spin coupling constants derived from proton NMR studies of proteins have been examined. Trajectories obtained from molecular dynamics simulations of bovine pancreatic trypsin inhibitor and of hen egg white lysozyme were used in conjunction with an expression for the dependence of the coupling constant on the intervening dihedral angle to calculate the time-dependent behavior of the coupling constants. Despite large fluctuations, the time-average values of the coupling constants are not far from those computed for the average structure in the cases where fluctuations occur about a single potential well. The calculated differences show a high correlation with the variation in the magnitude of the fluctuations of individual dihedral angles. For the cases where fluctuations involve multiple sites, large differences are found between the time-average values and the average structure values for the coupling constants. Comparison of the simulation results with the experimental trends suggests that side chains with more than one position are more common in proteins than is inferred from X-ray results. It is concluded that for the main chain, motional effects do not introduce significant errors where vicinal coupling constants are used in structure determinations; however, for side chains, the motional average can alter deductions about the structure. Accurately measured coupling constants are shown to provide information concerning the magnitude of dihedral angle fluctuations.     

Sprinting with banked turns

Bank angle effects can attenuate peak running speed on the order of 10%. Experimental and theoretical results are presented here to quantify this phenomenon over a wide range of bank angles theta b and turn radii R. Experimentally, eleven subjects ran on a 34 m long plywood test track with variable radius and bank angle to sample the (R, theta b) space. From another study, ten subjects are borrowed to examine the theta b = 0 degrees case in greater detail. Various gait parameters were measured from high-speed film, and after parallax correction, compared with the theoretical predictions. The theory is a simple two-parameter constant force model requiring only the effective ankle pulley ratio beta and the runner's top speed vm. A closed-form dimensionless solution is presented for the speed ratio (v/vm) as a function of the radius number (Rg/v2) and the bank angle theta b. Agreement between theory and experiment is limited by experimental scatter. For twenty different subjects and twelve different combinations of R and theta b, the apparent ankle pulley ratio is beta = 0.27 +/- 0.22 based on 128 separate trials. Applications are discussed briefly for the design of indoor and outdoor running tracks. The theory allows a calculation of foot force, bone force, and tendon tension for the general case of arbitrary maximum speed, turn radius and bank angle.     

The lysosome turns fifty

In the course of an investigation aimed at characterizing hepatic glucose 6-phosphatase, the unrelated acid phosphatase of rat liver was serendipitously observed to be latent and particle-bound in freshly prepared homogenates. Experiments designed to elucidate this intriguing finding led, 50 years ago, to the discovery of lysosomes. This could not have happened if strict adherence to a previously set programme had been mandatory.