Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase

Characterization of the putative tryptophan synthase beta-subunit from Mycobacterium tuberculosis

The increasing emergence of drug-resistant tuberculosis (TB) poses a serious threat to the control of this disease. It is in urgent need to develop new TB drugs. Tryptophan biosynthetic pathway plays an important role in the growth and replication of Mycobacterium tuberculosis (Mtb). The beta-subunit of tryptophan synthase (TrpB) catalyzes the last step of the tryptophan biosynthetic pathway, and it might be a potential target for TB drug design. In this study, we overexpressed, purified, and characterized the putative TrpB-encoding gene Rv1612 in Mtb H37Rv. Results showed that Mtb His-TrpB optimal enzymatic activity is at pH 7.8 with 0.15 M Na(+) or 0.18 M Mg(2+) at 37 degrees C. Structure analysis indicated that Mtb TrpB exhibited a typical beta/alpha barrel structure. The amino acid residues believed to interact with the enzyme cofactor pyridoxal-5'-phosphate were predicted by homology modeling and structure alignment. The role of these residues in catalytic activity of the Mtb His-TrpB was confirmed by site-directed mutagenesis. These results provided reassuring structural information for drug design based on TrpB.

Tritium planigraphy: from the accessible surface to the spatial structure of a protein

The method of tritium planigraphy, which provides comprehensive information on the accessible surface of macromolecules, allows an attempt at reconstructing the three-dimensional structure of a protein from the experimental data on residue accessibility for labeling. The semiempirical algorithm proposed for globular proteins involves (i) predicting theoretically the secondary structure elements (SSEs), (ii) experimentally determining the residue-accessibility profile by bombarding the whole protein with a beam of hot tritium atoms, (iii) generating the residue-accessibility profiles for isolated SSEs by computer simulation, (iv) locating the contacts between SSEs by collating the experimental and simulated accessibility profiles, and (v) assembling the SSEs into a compact model via these contact regions in accordance with certain rules. For sperm whale myoglobin, carp and pike parvalbumins, the lambda cro repressor, and hen egg lysozyme, this algorithm yields the most realistic models when SSEs are assembled sequentially from the amino to the carboxyl end of the protein chain.

Prediction and evaluation of side-chain conformations for protein backbone structures

A common approach to protein modeling is to propose a backbone structure based on homology or threading and then to attempt to build side chains onto this backbone. A fast algorithm using the simple criteria of atomic overlap and overall rotamer probability is proposed for this purpose. The method was first tested in the context of exhaustive searches of side chain configuration space in protein cores and was then applied to all side chains in 49 proteins of known structure, using simulated annealing to sample space. The latter procedure obtains the correct rotamer for 57% and the correct chi 1 value for 74% of the 6751 residues in the sample. When low-temperature Monte-Carlo simulations are initiated from the results of the simulated-annealing processes, consensus configurations are obtained which exhibit slightly more accurate predictions. The Monte-Carlo procedure also allows converged side chain entropies to be calculated for all residues. These prove to be accurate indicators of prediction reliability. For example, the correct rotamer is obtained for 79% and the correct chi 1 value is obtained for 84% of the half of the sample residues exhibiting the lowest entropies. Side chain entropy and predictability are nearly completely uncorrelated with solvent-accessible area. Some precedents for and implications of this observation are discussed.

Scrapie prions: a three-dimensional model of an infectious fragment

BACKGROUND

A conformational change seems to represent the major difference between the scrapie prion protein (PrPSc) and its normal cellular isoform (PrPC). We recently proposed a set of four helix bundle models for the three-dimensional structure of PrPC that are consistent with a variety of spectroscopic and genetic data.

RESULTS

We report a plausible model for the three-dimensional structure of a biologically important fragment of PrPSc. The model of residues 108-218 was constructed by an approach that combines computational techniques and experimental data. The proposed structures of this fragment of PrPSc display a four-stranded beta-sheet covered on one face by two alpha-helices. Residues implicated in the prion species barrier are found to cluster on the solvent-accessible surface of the beta-sheet of one of the models. This interface could provide a structural template that would assist the conversion of PrPC to PrPSc and hence direct prion propagation.

CONCLUSIONS

Molecular models of the PrP isoforms should prove very useful in developing structural hypotheses about the process by which PrPC is transformed into PrPSc, the mechanisms by which PrP gene mutations give rise to the inherited human prion diseases, and the species barrier that seems to protect humans from animal prions. It seems likely that PrPC represents a kinetically trapped intermediate in PrP folding.

Structure of the hormone binding domain of human beta 1 thyroid hormone nuclear receptor: is it an alpha/beta barrel?

To understand the structure of the hormone binding domain (HBD) of human beta 1 thyroid hormone nuclear receptor (h-TR beta 1), truncated h-TR beta 1 fragments, MD32 (M169-D456), KD29 (K201-D456), DD28 (D211-D456), KD25 (K235-D456), and KP28 (K201-P448), were analyzed by circular dichorism (CD). MD32 and KD29 show intense CD spectra with double minima at 222 and 208-210 nm, indicating the presence of extensive regions of alpha-helix. DD28 and KD25 have spectra which are reduced in intensity with minima around 215 nm, characteristic of a beta-sheet. The observed spectra are compatible with sequence analysis which predicts that HBD contains alternating stretches of alpha-helix and beta-strand. These extensive decreases in secondary structure in DD28 and KP28 in which the predicted first beta-strand or last alpha-helix was deleted, respectively, were accompanied by the loss of hormone binding activity. On the basis of these results, we suggest a new model for h-TR beta 1 consisting of the known DNA binding domain linked by an alpha-helical hinge to the HBD, with the tertiary structure of an alpha/beta barrel. The model is compatible with previous chemical and genetic studies on the structure of this protein.

Comparing the human and schistosomal hypoxanthine-guanine phosphoribosyltransferases by circular dichroism

The hypoxanthine-guanine phosphoribosyltransferases (HGPRTases) of human and the parasitic trematode, Schistosoma mansoni, are of biomedical importance. The conformations of these two enzymes were studied by circular dichroism (CD). The schistosomal HGPRTase is estimated to contain 27% alpha-helix and 30% beta-structure. This result is consistent with what is predicted from a tertiary model (Craig, S.P., Cohen, F.E., Yuan, L., McKerrow, J.H. and Wang, C.C. (1991) in Molecular & Immunological Aspects of Parasitism (Wang, C.C., ed.), pp. 122-138, Am. Assoc. Adv. Sci., Washington DC, USA), which proposes that the enzyme is an alpha/beta barrel protein. The human enzyme is estimated to contain 21% alpha-helix and 53% beta-form. The two enzymes are different in their thermostability. The human enzyme remains active after being heated to 85 degrees C for 15 min, while the schistosomal enzyme only retains its activity at temperature below 65 degrees C. The transition temperature (T1/2) of the schistosomal HGPRTase was determined by CD measurement to be 57.5 degrees C. One of the enzyme substrates, phosphoribose pyrophosphate (PRPP), stabilizes the HGPRTases by preventing the human enzyme from unfolding at 85 degrees C and partially protecting the schistosomal enzyme from unfolding at 65 degrees C. It is suggested that the amino-acid substitutions in the human enzyme improve the spatial structure and stability of its alpha-helices, which may lead to an enhanced thermostability.

Experimental and theoretical studies of the three-dimensional structure of human interleukin-4

The structure of human interleukin 4 (IL-4) was predicted utilizing a series of experimental and theoretical techniques. Circular Dichroism (CD) spectroscopy indicated that IL-4 belonged to the all alpha-helix class of protein structures. Secondary structure prediction, site-directed mutagenesis, and CD spectroscopy suggested a predominantly alpha-helical structure, consistent with a four-helix bundle structural motif. A human/mouse IL-4 chimera was constructed to qualitatively evaluate alternative secondary structure predictions. The four predicted helices were assembled into tertiary structures using established algorithms. The mapping of three disulfide bridges in IL-4 provided additional constraints on possible tertiary structures. Using accessible surface contact area as a criterion, the most suitable structures were right handed all antiparallel four-helix bundles with two overhand loop connections. Successful loop closure and incorporation of the three disulfide constraints were possible while maintaining the expected shape, solvent accessibility, and steric interactions between loops and helices. Lastly, energy minimization was used to regularize the chain.

A knowledge-based architecture for protein sequence analysis and structure prediction

Methods for analyzing the amino-acid sequence of a protein for the purposes of predicting its three-dimensional structure were systematically analyzed using knowledge engineering techniques. The resulting entities (data) and relations (processing methods and constraints) have been represented within a generalized dependency network consisting of 29 nodes and over 100 links. It is argued that such a representation meets the requirements of knowledge-based systems in molecular biology. This network is used as the architecture for a prototype knowledge-based system that simulates logically the processes used in protein structure prediction. Although developed specifically for applications in protein structure prediction, the network architecture provides a strategy for tackling the general problem of orchestrating and integrating the diverse sources of knowledge that are characteristic of many areas of science.

Protein conformational prediction

The prediction of the secondary and tertiary structure of globular and membrane proteins is reviewed. Prospects are encouraging for future developments, but present algorithms require cautious interpretation.

Tertiary structure of plant RuBisCO: domains and their contacts

The three-dimensional structure of ribulose-1,5-biphosphate carboxylase-oxygenase (RuBisCO), has been determined at 2.6 A resolution. This enzyme initiates photosynthesis by combining carbon dioxide with ribulose bisphosphate to form two molecules of 3-phosphoglycerate. In plants, RuBisCO is built from eight large (L) and eight small (S) polypeptide chains, or subunits. Both S chains and the NH2-terminal domain (N) of L are antiparallel beta, "open-face-sandwich" domains with four-stranded beta sheets and flanking alpha helices. The main domain (B) of L is an alpha/beta barrel containing most of the catalytic residues. The active site is in a pocket at the opening of the barrel that is partly covered by the N domain of a neighboring L chain. The domain contacts of the molecule and its conserved residues are discussed in terms of this structure.