Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.

This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA and then identifying the free energy minima common to all folded sequences via simultaneous clustering of the independent folding runs. Global measures of hydrophobic core formation, using ellipsoidal rather than spherical representations of the hydrophobic core, are found to be useful in removing non-native conformations before cluster analysis. Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set. Proteins 2001;43:1-11.

Rosetta in CASP4: progress in ab initio protein structure prediction.

Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 A) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fold largely correct were produced for several targets with new folds, and for several difficult fold recognition targets, the Rosetta models were more accurate than those produced with traditional fold recognition models. These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information.

De novo protein structure determination using sparse NMR data.

We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with approximately 1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined.

High-speed random access laser tuning.

We have developed a technique for laser tuning at rates of 100 kHz or more using a pair of acousto-optic modulators. In addition to all-electronic wavelength control, the same modulators also can provide electronically variable Q-switching, cavity length and power stabilization, chirp and linewidth control, and variable output coupling, all at rates far beyond what is possible with conventional mechanically tuned components. Tuning rates of 70 kHz have been demonstrated on a radio-frequency-pumped CO2 laser, with random access to over 50 laser lines spanning a 17% range in wavelength and with wavelength discrimination better than 1 part in 1000. A compact tuner and Q-switch has been deployed in a 5-10-kHz pulsed lidar system. The modulators each operate at a fixed Bragg angle, with the acoustic frequency determining the selected wavelength. This arrangement doubles the wavelength resolution without introducing an undesirable frequency shift.

Lessons from medical treatment of Army Reserve units during annual training.

During annual training, a reserve hospital unit staffed a clinic, providing sick-call for its own members and secondary care for about 3,000 National Guard soldiers. Reservists reporting for sick call were treated predominantly for respiratory infection, while the Guard members complained most frequently of field-related injuries. Quality assurance (QA) was done by the authors to evaluate handling of sick call over the 2 weeks, and few problems emerged upon review of the clinic records. Suggestions for future years include establishing standard terminology for recording chief complaint and discharge disposition, and the use of treatment guidelines for training and QA purposes.

Synthetic-array heterodyne detection: a single-element detector acts as an array.

A simple technique, synthetic-array heterodyne detection, permits an ordinary single-element optical detector to behave as though it were a coherent array. A successful experimental implementation of a synthetic two-pixel array, using a CO(2) laser and a single-element HgCdTe photodiode is reported. A different heterodyne local oscillator frequency is incident upon each resolvable region of the detector surface. Thus different regions are mapped to different heterodyne beat frequencies. One can determine where the photons struck the detector surface even though a single electrical connection to the detector is used. This also prevents the destructive interference that occurs when multiple speckles are imaged (akin to spatial diversity). In coherent lidar this permits a larger field of view. An acousto-optic modulator produces the local oscillator frequencies and can achieve good spatial separation of optical frequencies of the order of a megahertz apart.

Broadly tunable difference-frequency generation of VUV using two-photon resonances in H(2) and Kr.

We report generation of tunable VUV radiation in the range 117-150 nm by four-wave difference-frequency mixing of a tunable ArF excimer laser with an Nd:YAG-pumped dye laser. The four-wave mixing occurs through two-photon resonant enhancement of X((3)) through the E,F(1)Sigma(g)+ (E,' = 2, J' = 0-3) state(s) of H(2) or the 4p(5)6p(3/2)(2) state of Kr in the process (2omega(193) - omega(dye) = omega(VUV)). An estimate of energy efficiency yields 3 x 10(-5) near 133 nm for both H(2) and Kr. Even though several rotational resonances fall within the natural 193-nm bandwidth, mixing with broadband ArF output in H(2) yields single-line VUV output with a FWHM of 3.5 cm(-1) at half the efficiency compared with that of line-narrowed operation.