The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: Insights for a new classification of snake venom metalloprotease subgroups

Bothropasin is a 48 kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys(189) is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from I`ll SVMPs. The ECD motif is stabilized by the Cys(117)_Cys(310) disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu(276) of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other Pill SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other Pill members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain. (C) 2008 Elsevier Ltd. All rights reserved.

Isolation and characterization of four type 2 ribosome inactivating pulchellin isoforms from Abrus pulchellus seeds

Abrus pulchellus seeds contain at least seven closely related and highly toxic type 2 ribosome-inactivating pulchellins, each consisting of a toxic A-chain linked to a sugar binding B-chain. In the present study, four pulchellin isoforms (termed P I, P II, P III and P IV) were isolated by affinity, ion exchange and chromatofocusing chromatographies, and investigated with respect to toxicity and sugar binding specificity. Half maximal inhibitory concentration and median lethal dose values indicate that P I and P II have similar toxicities and that both are more toxic to cultured HeLa cells and mice than P III and P IV. Interestingly, the secondary structural characteristics and sugar binding properties of the respective pairs of isoforms correlate well with the two toxicity levels, in that P I/P II and P III/P IV form two specific subgroups. From the deduced amino acids sequences of the four isoforms, it is clear that the highest similarity within each subgroup is found to occur within domain 2 of the B-chains, suggesting that the disparity in toxicity levels might be attributed to subtle differences in B-chain-mediated cell surface interactions that precede and determine toxin uptake pathways.

PARALLEL ALGORITHMS FOR MAXIMAL CLIQUES IN CIRCLE GRAPHS AND UNRESTRICTED DEPTH SEARCH

We present parallel algorithms on the BSP/CGM model, with p processors, to count and generate all the maximal cliques of a circle graph with n vertices and m edges. To count the number of all the maximal cliques, without actually generating them, our algorithm requires O(log p) communication rounds with O(nm/p) local computation time. We also present an algorithm to generate the first maximal clique in O(log p) communication rounds with O(nm/p) local computation, and to generate each one of the subsequent maximal cliques this algorithm requires O(log p) communication rounds with O(m/p) local computation. The maximal cliques generation algorithm is based on generating all maximal paths in a directed acyclic graph, and we present an algorithm for this problem that uses O(log p) communication rounds with O(m/p) local computation for each maximal path. We also show that the presented algorithms can be extended to the CREW PRAM model.

The C(K, X) spaces for compact metric spaces K and X with a uniformly convex maximal factor

In this paper, we prove that if a Banach space X contains some uniformly convex subspace in certain geometric position, then the C(K, X) spaces of all X-valued continuous functions defined on the compact metric spaces K have exactly the same isomorphism classes that the C(K) spaces. This provides a vector-valued extension of classical results of Bessaga and Pelczynski (1960) [2] and Milutin (1966) [13] on the isomorphic classification of the separable C(K) spaces. As a consequence, we show that if 1 < p < q < infinity then for every infinite countable compact metric spaces K(1), K(2), K(3) and K(4) are equivalent: (a) C(K(1), l(p)) circle plus C(K(2), l(q)) is isomorphic to C(K(3), l(p)) circle plus (K(4), l(q)). (b) C(K(1)) is isomorphic to C(K(3)) and C(K(2)) is isomorphic to C(K(4)). (C) 2011 Elsevier Inc. All rights reserved.

Towards a maximal extension of Pelczynski`s decomposition method in Banach spaces

l Suppose that X, Y. A and B are Banach spaces such that X is isomorphic to Y E) A and Y is isomorphic to X circle plus B. Are X and Y necessarily isomorphic? In this generality. the answer is no, as proved by W.T. Cowers in 1996. In the present paper, we provide a very simple necessary and sufficient condition on the 10-tuples (k, l, m, n. p, q, r, s, u, v) in N with p+q+u >= 3, r+s+v >= 3, uv >= 1, (p,q)$(0,0), (r,s)not equal(0,0) and u=1 or v=1 or (p. q) = (1, 0) or (r, s) = (0, 1), which guarantees that X is isomorphic to Y whenever these Banach spaces satisfy X(u) similar to X(p)circle plus Y(q), Y(u) similar to X(r)circle plus Y(s), and A(k) circle plus B(l) similar to A(m) circle plus B(n). Namely, delta = +/- 1 or lozenge not equal 0, gcd(lozenge, delta (p + q - u)) divides p + q - u and gcd(lozenge, delta(r + s - v)) divides r + s - v, where 3 = k - I - in + n is the characteristic number of the 4-tuple (k, l, m, n) and lozenge = (p - u)(s - v) - rq is the discriminant of the 6-tuple (p, q, r, s, U, v). We conjecture that this result is in some sense a maximal extension of the classical Pelczynski`s decomposition method in Banach spaces: the case (1, 0. 1, 0, 2. 0, 0, 2. 1. 1). (C) 2009 Elsevier Inc. All rights reserved.

SIGMA THEORY AND TWISTED CONJUGACY CLASSES

Using Sigma theory we show that for large classes of groups G there is a subgroup H of finite index in Aut(G) such that for phi is an element of H the Reidemeister number R(phi) is infinite. This includes all finitely generated nonpolycyclic groups G that fall into one of the following classes: nilpotent-by-abelian groups of type FP(infinity); groups G/G `` of finite Prufer rank; groups G of type FP(2) without free nonabelian subgroups and with nonpolycyclic maximal metabelian quotient; some direct products of groups; or the pure symmetric automorphism group. Using a different argument we show that the result also holds for 1-ended nonabelian nonsurface limit groups. In some cases, such as with the generalized Thompson`s groups F(n,0) and their finite direct products, H = Aut(G).

Locally nilpotent groups of units in tiled rings

We consider locally nilpotent subgroups of units in basic tiled rings A, over local rings O which satisfy a weak commutativity condition. Tiled rings are generalizations of both tiled orders and incidence rings. If, in addition, O is Artinian then we give a complete description of the maximal locally nilpotent subgroups of the unit group of A up to conjugacy. All of them are both nilpotent and maximal Engel. This generalizes our description of such subgroups of upper-triangular matrices over O given in M. Dokuchaev, V. Kirichenko, and C. Polcino Milies (2005) [3]. (C) 2010 Elsevier Inc. All rights reserved.

All maximal-pairs in step-leap representation of melodic sequence

This paper proposes an efficient pattern extraction algorithm that can be applied on melodic sequences that are represented as strings of abstract intervallic symbols; the melodic representation introduces special “binary don’t care” symbols for intervals that may belong to two partially overlapping intervallic categories. As a special case the well established “step–leap” representation is examined. In the step–leap representation, each melodic diatonic interval is classified as a step (±s), a leap (±l) or a unison (u). Binary don’t care symbols are used to represent the possible overlapping between the various abstract categories e.g. *=s, *=l and #=-s, #=-l. We propose an O(n+d(n-d)+z)-time algorithm for computing all maximal-pairs in a given sequence x=x[1..n], where x contains d occurrences of binary don’t cares and z is the number of reported maximal-pairs.

All maximal-pairs in step-leap representation of melodic sequence

This paper proposes an efficient pattern extraction algorithm that can be applied on melodic sequences that are represented as strings of abstract intervallic symbols; the melodic representation introduces special “binary don’t care” symbols for intervals that may belong to two partially overlapping intervallic categories. As a special case the well established “step–leap” representation is examined. In the step–leap representation, each melodic diatonic interval is classified as a step (±s), a leap (±l) or a unison (u). Binary don’t care symbols are used to represent the possible overlapping between the various abstract categories e.g. *=s, *=l and #=-s, #=-l. We propose an O(n+d(n-d)+z)-time algorithm for computing all maximal-pairs in a given sequence x=x[1..n], where x contains d occurrences of binary don’t cares and z is the number of reported maximal-pairs.