Small libraries of protein fragments model native protein structures accurately

Prediction of protein structure depends on the accuracy and complexity of the models used. Here, we represent the polypeptide chain by a sequence of rigid fragments that are concatenated without any degrees of freedom. Fragments chosen from a library of representative fragments are fit to the native structure using a greedy build-up method. This gives a one-dimensional representation of native protein three-dimensional structure whose quality depends on the nature of the library. We use a novel clustering method to construct libraries that differ in the fragment length (four to seven residues) and number of representative fragments they contain (25-300). Each library is characterized by the quality of fit (accuracy) and the number of allowed states per residue (complexity). We find that the accuracy depends on the complexity and varies from 2.9A for a 2.7-state model on the basis of fragments of length 7-0.76A for a 15-state model on the basis of fragments of length 5. Our goal is to find representations that are both accurate and economical (low complexity). The models defined here are substantially better in this regard: with ten states per residue we approximate native protein structure to 1A compared to over 20 states per residue needed previously.For the same complexity, we find that longer fragments provide better fits. Unfortunately, libraries of longer fragments must be much larger (for ten states per residue, a seven-residue library is 100 times larger than a five-residue library). As the number of known protein native structures increases, it will be possible to construct larger libraries to better exploit this correlation between neighboring residues. Our fragment libraries, which offer a wide range of optimal fragments suited to different accuracies of fit, may prove to be useful for generating better decoy sets for ab initio protein folding and for generating accurate loop conformations in homology modeling.     

Sequence variations within protein families are linearly related to structural variations

It is commonly believed that similarities between the sequences of two proteins infer similarities between their structures. Sequence alignments reliably recognize pairs of protein of similar structures provided that the percentage sequence identity between their two sequences is sufficiently high. This distinction, however, is statistically less reliable when the percentage sequence identity is lower than 30% and little is known then about the detailed relationship between the two measures of similarity. Here, we investigate the inverse correlation between structural similarity and sequence similarity on 12 protein structure families. We define the structure similarity between two proteins as the cRMS distance between their structures. The sequence similarity for a pair of proteins is measured as the mean distance between the sequences in the subsets of sequence space compatible with their structures. We obtain an approximation of the sequence space compatible with a protein by designing a collection of protein sequences both stable and specific to the structure of that protein. Using these measures of sequence and structure similarities, we find that structural changes within a protein family are linearly related to changes in sequence similarity.     

NAD binding induces conformational changes in Rho ADP-ribosylating clostridium botulinum C3 exoenzyme

We have solved the crystal structures of Clostridium botulinum C3 exoenzyme free and complexed to NAD in the same crystal form, at 2.7 and 1.95 A, respectively. The asymmetric unit contains four molecules, which, in the free form, share the same conformation. Upon NAD binding, C3 underwent various conformational changes, whose amplitudes were differentially limited in the four molecules of the crystal unit. A major rearrangement concerns the loop that contains the functionally important ARTT motif (ADP-ribosyltransferase toxin turn-turn). The ARTT loop undergoes an ample swinging motion to adopt a conformation that covers the nicotinamide moiety of NAD. In particular, Gln-212, which belongs to the ARTT motif, flips over from a solvent-exposed environment to a buried conformation in the NAD binding pocket. Mutational experiments showed that Gln-212 is neither involved in NAD binding nor in the NAD-glycohydrolase activity of C3, whereas it plays a critical role in the ADP-ribosyl transfer to the substrate Rho. We observed additional NAD-induced movements, including a crab-claw motion of a subdomain that closes the NAD binding pocket. The data emphasized a remarkable NAD-induced plasticity of the C3 binding pocket and suggest that the NAD-induced ARTT loop conformation may be favored by the C3-NAD complex to bind to the substrate Rho. Our structural observations, together with a number of mutational experiments suggest that the mechanisms of Rho ADP-ribosylation by C3-NAD may be more complex than initially anticipated.     

Mechanisms of flavonoid repair reactions with amino acid radicals in models of biological systems: a pulse radiolysis study in micelles and human serum albumin

Neutral tryptophan (*Trp) and tyrosine (TyrO(*)) radicals are repaired by certain flavonoids in buffer, in micelles and in human serum albumin (HSA) with corresponding formation of semioxidized flavonoid radicals. In deaerated buffer, *Trp but not TyrO(*) radicals react with catechin. In micelles, quercetin and rutin repair both *Trp and TyrO(*) radicals. In addition to amino acid reactivity, microenvironmental factors and nature of the flavonoids govern this repair. Electron transfer efficiencies from quercetin to negatively charged *Trp radicals are 100% in the micellar pseudophases of positively charged cetyltrimethylammonium bromide, (CTAB), and neutral Triton X100 (TX100), but 55% in negatively charged sodium dodecyl sulfate (SDS). In oxygen-saturated CTAB micelles, quercetin also reacts with the superoxide radical anion. When bound to domain IIA of HSA, quercetin repairs, by intra- or intermolecular encounter, less than 20% of oxidative damage to HSA. Quercetin can also repair freely circulating oxidized molecules with repair efficiencies falling to 7% for oxidized *Trp, Tyr and alpha-MSH and to less than 2% for urate radical. This limited effectiveness is attributed both to the inaccessibility of bound quercetin and rutin toward radicals of circulating molecules and to the diffusion-controlled recombination of these radicals.     

Herd size in large herbivores: encoded in the individual or emergent?

In large mammalian herbivores, the increase of group size with habitat openness was first assumed to be an adaptive response, encoded in the individual. However, it could, alternatively, be an emergent property: if groups were nonpermanent units, often fusing and splitting up, then any increase of the distance at which animals perceive one another could increase the rate of group fusion and thus mean group size. Dynamical models and empirical data support this second hypothesis. This is not to say that adaptive modifications of mean herd size cannot occur. However, this changes the way in which we can envisage the history of gregariousness in large herbivores during the Tertiary.     

Hazards,threats and risks: lessons from the past to a defensive attitude for the future

Since ever infectious diseases have been a major hazard for the armed forces in operations. Nowadays our nations are facing the threat of terrorism, including bioterrorism. This threat is much more related to the potential disorganization of the society than to the lethal effects of the agents. Biological weapons are considered more like terror weapons than like mass destruction weapons, hence the importance of preparing specific defence measures. The know-how acquired from the struggle against natural infectious diseases is a useful help to face the biological weapon threats and risks. Likewise, the defence attitude is based on three pillars: anticipating, managing, and restoring. This military as well as civilian defence attitude applies to six important functions: (1) alert, (2) detection, diagnosis and identification, (3) medical countermeasures (drugs, vaccines and sera), (4) medical care in hospital, (5) training and information, (6) research and development of dedicated technologies.     

Multiplicative genetic effects in scrapie disease susceptibility

Despite experimental evidence that scrapie is an infectious disease of sheep, variations of the occurrence of the natural disease suggest an influence of host genetic factors. It has been established that the genetic polymorphism of the prion protein (PrP) gene is correlated to the incidence of scrapie and to the survival time: five polymorphisms have been described by variations at amino-acid codons 136, 154 and 171. In this paper we study the effect on scrapie susceptibility of the pairing of the five allelic variants known to exist: we show that scrapie susceptibility is given by the produce of the elementary allelic factors. This first well-documented evidence of a multiplicative property of genetic risk factors could give hints on the underlying mechanisms of prion-induced neurodegenerative diseases.     

Spontaneous polar anterior subcapsular lenticular opacity in Sprague-Dawley rats

A spontaneous focal polar anterior subcapsular lenticular opacity characterized by focal epithelial proliferation was found in Charles River Sprague-Dawley rats from various breeding facilities around the world (France, Japan, and the United States). The incidence of this change slightly increased with age up to a maximal incidence of 9.8% in 28- to 35-week-old male rats (French source). Over that period, there was little change in the size of the opacity; however some rats that were examined over longer periods (more than 2 years of age) developed secondary anterior cortical changes, and rarely, histologic findings of pigmentation and/or mineralization. The lenticular change was present throughout the life of the animals and had no sex predilection; mode of inheritance was not investigated. Due to its small size, this lens opacity is more easily identified by use of slit lamp biomicroscopy than by use of indirect ophthalmoscopy, and serial sections of the eye aid in locating it for histologic evaluation.     

Connexin 32 fused to the green fluorescent protein retains its ability to control the proliferation of thyroid cells

Cell-to-cell exchanges of signaling molecules are thought to be involved in the control of cell proliferation. Connexins, which are encoded by a family of genes expressed in a cell type-specific manner, are considered as tumor suppressors. Thyroid epithelial cells co-express connexin 32 (Cx32) and connexin 43 (Cx43) that form distinct and delocalized gap junctions in vivo. The communication-deficient rat thyroid-derived cell lines, FRTL-5 and FRT, stably transfected with the Cx32 cDNA, have a reduced proliferation rate related to a prolonged G1 cell cycle phase. To determine whether Cx32-gap junctions exert the same regulatory role in vivo, we have undertaken a program of production of transgenic mice over-expressing Cx32 specifically in thyrocytes. To this purpose, we designed a vector in which the Cx32 cDNA was fused to the gene encoding the enhanced green fluorescent protein (EGFP) and placed under the control of a strong and thyroid-specific promoter, the thyroglobulin gene promoter (pTg). In stably transfected FRTL-5 cells, the Cx32/EGFP chimeric protein forms functional gap junction channels and induces the same proliferation slowdown as native Cx32. The pTg-Cx32/EGFP construct should thus allow us to obtain the thyroid-targeted over-expression of Cx32 in the mouse to investigate the involvement of Cx32-gap junctions in thyroid growth, functional activity and propensity to form tumors.