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Although the human and Plasmodium enzymes share 42% amino acid sequence identity, several key differences suggest that PfTIM may turn out to be a potential drug target. We have identified a region which may be responsible for binding PfTIM to cytoskeletal elements or the band 3 protein of erythrocytes; attachment to the erythrocyte membrane may subsequently lead to the extracellular exposure of parts of the protein. This feature may be important in view of a recent report that patients suffering from P. falciparum malaria mount an antibody response to TIM leading to prolonged hemolysis. A second approach to drug design may be provided by the mutation of the largely conserved residue (Ser96) to phenylalanine in PfTIM. This difference may be of importance in designing specific active-site inhibitors against the enzyme. Finally, specific inhibition of PfTIM subunit assembly might be possible by targeting Cys13 at the dimer interface. The crystal structure of PfTIM provides a framework for new therapeutic leads.

The factors contributing to the thermal stability of proteins from thermophilic origins are matters of intense debate and investigation. Thermophilic proteins are thought to possess better packed interiors than their mesophilic counterparts, leading to lesser overall flexibility and a corresponding reduction in surface-to-volume ratio. These observations prompted an analysis of B values reported in high-resolution X-ray crystal structures of mesophilic and thermophilic proteins. In this analysis, the following aspects were addressed: (1) frequency distribution of normalized B values (B' factors) over all the proteins and for individual amino acids; (2) amino acid compositions in high B value regions of polypeptide chains; (3) variation in the B values from core to the surface of proteins in terms of their radius of gyration; and (4) degree of dispersion of normalized B values in spheres around the Calpha atoms. The analysis revealed that (1) Ser and Thr have lesser flexibility in thermophiles than in mesophiles, (2) the proportion of Glu and Lys in high B value regions of thermophiles is higher and that of Ser and Thr is lower and (3) the dispersion of B values within spheres at Calpha atoms is similar in mesophiles and thermophiles. These observations reflect plausible differences in the dynamics of thermophilic and mesophilic proteins and suggest amino acid substitutions that are likely to change thermal stability.

Catalase (hydrogen peroxide:hydrogen-peroxide oxidoreductase, EC 1.11.1.6) occurs in almost all aerobically respiring organisms and in part serves to protect cells from the toxic effects of hydrogen peroxide. The subcellular location of liver catalase is restricted to the peroxisomes, and the enzyme is probably incorporated into these organelles during their biogenesis (1). The properties of catalase have been reviewed by numerous authors including Deisseroth and Dounce (2) and Schonbaum and Chance (3). The overall reaction catalyzed by the enzyme can be written as ROOH + HQOH = QO + ROH + H20, [1] where R is H or an alkyl or acyl group and HQOH is a twoelectron donor in which Q is 0, C=O, or H(CH2)nCH (n = 1, 2, or 3). This reaction proceeds by two steps: (i) oxidation ofthe enzyme (E) by a peroxide E-H20 + ROOH = E-O + ROH + H20, [2] apocatalase I and (ii) oxidation of the substrate E-O + HQOH = E-H20 + QO.

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that of Macrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.

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The temperature factors obtained from X-ray refinement of proteins at high resolution show large variations from one structure to another. However, the B-values expressed in units of standard deviation about their mean value @'-factor) at the Ccu atoms show remarkably characteristic frequency distribution. In all of the 1 I O proteins examined in this study, the frequency distribution exhibited a bimodal distribution. The peaks in the B'-factor frequency distribution occur at -1.1 and 0.4 for a bin size of 0.5. The peak at lower temperature factor corresponds largely to buried residues, whereas the peak at larger value corresponds to exposed residues. The distribution could be accurately described as a superposition of two Gaussian functions. The parameters describing the distribution are therefore characteristic of protein structures. The frequency distribution for a given amino acid over all the proteins also shows a similar bimodal distribution, although the areas under the two Gaussians differ from one amino acid to another. The area under the frequency distribution curve for any interval in B'-factor represents the propensity of the amino acid to occur in that interval. This propensity is related both to the hydrophilicity/hydrophobicity of the residue and the tendency of the residue to impose a different degree of rigidity on the polypeptide chain. The frequency distribution of stretches of high B'-factors departs appreciably from that expected for a random distribution. The correlation in the B-values of sequentially proximal residues is probably responsible for the bimodal distribution.Keywords: accessibility; Gaussian functions; proteins; statistics; temperature factors Statistical analysis has formed a large component of the research efforts put forth to understand protein structure and function, due to the enormous diversity and complexity of their structures (Johnson et al., 1994). Statistical approaches have been developed to predict the secondary structure from the primary sequence (Chou & Fasman 1974; Gamier et al., 1978; Gamier, 1990) and for testing the compatibility of model tertiary folds for a given sequence of unknown structure (Bowie et al., 1991;Luthy et al., 1991Luthy et al., , 1992. A variety of statistical analyses has also been performed on conformational states of main chains and side chains (Dunbrack & Karplus, 1993), hydrogen bonding (Ippolito et al., 1990), water structure (Thanki et al., 1991), and topological features of secondary structural elements (Levitt & Chothia, 1976;Taylor & Thomton, 1983). Most of these analyses are concerned with protein structure and conformation. In contrast, much less attention has been paid to the atomic displacement parameter (Trueblood et al., 1996), B-values obtained from X-ray crystal structure analysis of proteins. The efforts in this direction have been concerned mainly with optimizing methods for prediction of antigenicity and flexibility of different polypeptide segments of a protein (Ragone et al., Reprint requests to: M.R.N. Murth...

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