Computational method to reduce the search space for directed protein evolution

We introduce a computational method to optimize the in vitro evolution of proteins. Simulating evolution with a simple model that statistically describes the fitness landscape, we find that beneficial mutations tend to occur at amino acid positions that are tolerant to substitutions, in the limit of small libraries and low mutation rates. We transform this observation into a design strategy by applying mean-field theory to a structure-based computational model to calculate each residue's structural tolerance. Thermostabilizing and activity-increasing mutations accumulated during the experimental directed evolution of subtilisin E and T4 lysozyme are strongly directed to sites identified by using this computational approach. This method can be used to predict positions where mutations are likely to lead to improvement of specific protein properties.

Direct observation of the oceanic CO2 increase revisited

We show, from recent data obtained at specimen North Pacific stations, that the fossil fuel CO2 signal is strongly present in the upper 400 m, and that we may consider areal extrapolations from geochemical surveys to determine the magnitude of ocean fossil fuel CO2 uptake. The debate surrounding this topic is illustrated by contrasting reports which suggest, based upon atmospheric observations and models, that the oceanic CO2 sink is small at these latitudes; or that the oceanic CO2 sink, based upon oceanic data and models, is large. The difference between these two estimates is at least a factor of two. There are contradictions arising from estimates based on surface partial pressures of CO2 alone, where the signal sought is small compared with regional and seasonal variability; and estimates of the accumulated subsurface burden, which correlates well other oceanic tracers. Ocean surface waters today contain about 45 μmol⋅kg−1 excess CO2 compared with those of the preindustrial era, and the signal is rising rapidly. What limits should we place on such calculations? The answer lies in the scientific questions to be asked. Recovery of the fossil fuel CO2 contamination signal from analysis of ocean water masses is robust enough to permit reasonable budget estimates. However, because we do not have sufficient data from the preindustrial ocean, the estimation of the required Redfield oxidation ratio in the upper several hundred meters is already blurred by the very fossil fuel CO2 signal we seek to resolve.

A method for distance determination in proteins using a designed metal ion binding site and site-directed spin labeling: evaluation with T4 lysozyme.

The use of molecular genetics to introduce both a metal ion binding site and a nitroxide spin label into the same protein opens the use of paramagnetic metalnitroxyl interactions to estimate intramolecular distances in a wide variety of proteins. In this report, a His-Xaa3-His metal ion binding motif was introduced at the N terminus of the long interdomain helix of T4 lysozyme (Lys-65 --> His/Gln-69 --> His) of three mutants, each containing a single nitroxide-labeled cysteine residue at position 71, 76, or 80. The results show that Cu(II)-induced relaxation effects on the nitroxide can be quantitatively analyzed in terms of interspin distance in the range of 10-25 A using Redfield theory, as first suggested by Leigh [Leigh, J.S. (1970) J. Chem. Phys. 52, 2608-2612]. Of particular interest is the observation that distances can be determined both under rigid lattice conditions in frozen solution and in the presence of motion of the spins at room temperature under physiological conditions. The method should be particularly attractive for investigating structure in membrane proteins that are difficult to crystallize. In the accompanying paper, the technique is applied to a polytopic membrane protein, lactose permease.