In this issue

1673 Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

Hsiau-Wei Lee, Greg Wylie, Sonal Bansal, Xu Wang, Adam W. Barb, Megan A. Macnaughtan, Asli Ertekin, Gaetano T. Montelione, and James H. Prestegard

Oligomeric protein structures are both common and functionally important in cellular biology. Yet, determination of oligomer structure is challenging, particularly in cases of weak association, and in NMR studies where degeneracies of resonances from different subunits complicate analysis. This article presents a straightforward means of assembling oligomeric protein structures using limited sets of NMR data from residual dipolar couplings (RDCs) and paramagnetic surface perturbations. The process is illustrated with determination of a homodimer structure for a previously uncharacterized 86 residue protein from Staphylococcus epidermidis (Q8CSK1).

1774 The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

Christoph Liebold, Felix List, Hans Robert Kalbitzer, Reinhard Sterner, and Eike Brunner

The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 enzyme complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5-aminoimidazole-4-carboxamide ribotide (AICAR). The aim of the present work is the elucidation of this process at a molecular level. The interaction of HisF with the noble gas xenon was analysed by solution NMR spectroscopy in order to detect and further characterize internal cavities/xenon-binding sites in HisF. It is shown that HisF contains three xenon-accessible internal cavities which might be of functional relevance. Solution NMR spectroscopy using NH₃/NH₄⁺ as a probe in addition to the reduced catalytic activity of the Thr78Met mutant indicate an important role of Thr78 in ammonia channelling.

1760 Evaluation and ranking of enzyme designs

Gert Kiss, Daniela Röthlisberger, David Baker, and K. N. Houk

Computational methods have been developed to design proteins that will catalyze non-natural chemical reactions. In the future, applications of the technology towards useful chemistry could be of considerable practical value to biotechnology, pharmacology, and chemical industries. The computational procedures are based on the quantum mechanical design of catalytic machineries and the Rosetta design of proteins to fold so as to produce suitable active sites. At present, the process generates large numbers of enzyme candidates, the overwhelming majority of which turn out to be inactive. This paper describes the development of a molecular dynamics (MD) computational strategy to distinguish active candidates from inactive ones prior to experiment. MD evaluation of candidate structures is also used together with experimentation to refine designs and to produce more active proteins. The paper further highlights that even the most active designer enzymes have considerable geometric deficiencies compared to naturally evolved enzymes, suggesting that there is much room for improvement.

1704 The human peripheral subunit-binding domain folds rapidly while overcoming repulsive Coulomb forces

Eyal Arbely, Hannes Neuweiler, Timothy D. Sharpe, Christopher M. Johnson, and Alan R. Fersht

Protein stability is often compromised by function. This article reveals a small human protein domain as a prime example of this paradigm. There are many charged side chains on the protein surface that are critical for function but greatly impair stability by repulsive Coulombic forces, which even induce changes in the native state. The protein folds in a few tens of μs in a classical manner even though being slowed down by the repulsive forces. Protein evolution is a trade-off between function and stability.