Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Spiroiminodihydantoin is the major product of the 8-oxo-7,8-dihydroguanosine reaction with peroxynitrite in the presence of thiols and guanosine photooxidation by methylene blue

[reaction: see text]. The potent oxidant, peroxynitrite, will oxidize 8-oxo-7,8-dihydroguanosine to give several products. In the presence of a thiol agent, the major final product has been determined to be a spiroiminodihydantoin compound. Additionally, we have found that the spiroiminodihydantoin, and not the previously reported 4-hydroxy-8-oxo-4,8-dihydroguanosine, is the major final product formed during the methylene blue-mediated photooxidation of guanosine.     

Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup

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Highlights? Recycling of genetic material is important for the origins of life ? Simulation studies show recycling leads to the selection of genotypes from a pool ? Recycling can lead to the sudden emergence of a high-fitness RNA genotype ? Experimental studies with the Azoarcus ribozyme show fragment recycling     

Labile clustering and its effects

A contour map of the minimum values for three-body rate constants and for equilibrium constants has been constructed for the initial three-body clustering of gas molecules to positive ions. The map was constructed from laboratory measurements of the clustering of gas molecules to alkali ions and consolidates into a readily useful form several recent measurements. Use of the map shows that labile clustering can be extremely important in laboratory experiments and in the earth's upper atmosphere.     

Selective C−H Functionalization of Methane and Ethane by a Molecular SbV Complex

Owing to the strong nonpolar bonds involved, selective C?H functionalization of methane and ethane to esters remains a challenge for molecular homogeneous chemistry. We report that the computationally predicted main‐group p‐block Sb^V(TFA)₅ complex selectively functionalizes the C?H bonds of methane and ethane to the corresponding mono and/or diol trifluoroacetate esters at 110–180 °C with yields for ethane of up to 60 % with over 90 % selectivity. Experimental and computational studies support a unique mechanism that involves Sb^V‐mediated C?H activation followed by functionalization of a Sb^V‐alkyl intermediate.     

Evolution finds shelter in small spaces

When RNA is replicated in cell-free systems, a ubiquitous problem is the hijacking of the system by short parasitic RNA sequences. In this issue of Chemistry & Biology, Bansho et?al. show that compartmentalization into water-in-oil droplets can ameliorate this problem, but only if the droplets are small. This result helps to both recapitulate abiogenesis and optimize synthetic biology.     

Dynamics of photon-induced degradation and fluorescence in riboflavin microparticles

An unexpected blue-fluorescence band (around 420 nm) from both micrometer-sized dried particles and aqueous droplets of riboflavin [7,8-dimethyl-10-(D-1^′-ribityl)-isoalloxazine] is observed when the microparticles are irradiated with a pulsed UV (355- or 351-nm) laser. The intensity of the band increases quadratically with input laser energy density (fluence) and is attributable to a one-photon-excited fluorescence of lumichrome (7,8-dimethyl-alloxazine) that is produced by photo-degradation of riboflavin. The well-known greenish-yellow fluorescence band (at 560 nm for dried particles and 535 nm for aqueous droplets) from riboflavin increases sublinearly with UV-laser fluence. With a laser input fluence above 5 J/cm² the riboflavin fluorescence decays earlier and the lumichrome fluorescence reaches a maximum later than the peak of the input laser pulse. The temporal dynamics of the 420- and 535-nm fluorescence peaks are consistent with a rate-equation simulation of photon-induced conversion of riboflavin to lumichrome and the subsequent fluorescence of lumichrome. Received: 28 September 2000 / Revised version: 11 December 2000 / Published online: 21 February 2001