Structural aspects of antibody-antigen interaction revealed through small random peptide libraries

Summary Two small random peptide libraries, one composed of 4550 dodecapeptides and one of 8000 tripeptides, were synthesized in newly developed credit-card format miniPEPSCAN cards (miniPEPSCAN libraries). Each peptide was synthesized in a discrete well (455 peptides/card). The two miniPEPSCAN libraries were screened with three different monoclonal antibodies (Mabs). Two other random peptide libraries, expressed on the wall of bacteria (recombinant libraries) and composed of 10⁷ hexa- and octapeptides, were screened with the same three Mabs. The aim of this study was to compare the amino acid sequence of peptides selected from small and large pools of random peptides and, in this way, investigate the potential of small random peptide libraries. The screening of the two miniPEPSCAN libraries resulted in the identification of a surprisingly large number of antibody-binding peptides, while the screening of the large recombinant libraries, using the same Mabs, resulted in the identification of only a small number of peptides. The large number of peptides derived from the small random peptide libraries allowed the determination of consensus sequences. These consensus sequences could be related to small linear and nonlinear parts of the respective epitopes. The small number of peptides derived from the large random peptide libraries could only be related to linear epitopes that were previously mapped using small libraries of overlapping peptides covering the antigenic protein. Thus, with respect to the cost and speed of identifying peptides that resemble linear and nonlinear parts of epitopes, small diversity libraries based on synthetic peptides appear to be superior to large diversity libraries based on expression systems.Abbreviations ABTS 2,2-azino-di-3-ethylbenzthiazoline sulfonate - EGF epidermal growth factor - Mab monoclonal antibody - OD_ccd optical density obtained using CCD camera - RAMPO rabbit-antimouse peroxidase - SDS sodium dodecylsulfate - TGEV transmissible gastroenteritis virus     

On the extreme spectral properties of Toeplitz matrices generated byL 1 functions with several minima/maxima

In this paper we are concerned with the asymptotic behavior of the smallest eigenvalue ₁ ⁽ⁿ⁾ of symmetric (Hermitian)n ×n Toeplitz matricesT _n (f) generated by an integrable functionf defined in [–, ]. In [7, 8, 11] it is shown that ₁ ⁽ⁿ⁾ tends to essinff =m _f in the following way: ₁ ⁽ⁿ⁾ –m _f 1/n ^2k . These authors use three assumptions:A1)f –m _f has a zero inx =x ₀ of order 2k.A2)f is continuous and at leastC ^2k in a neighborhood ofx ₀.A3)x =x ₀ is the unique global minimum off in [–, ]. In [10] we have proved that the hypothesis of smoothnessA2 is not necessary and that the same result holds under the weaker assumption thatf L ¹[–, ]. In this paper we further extend this theory to the case of a functionf L ¹[–, ] having several global minima by suppressing the hypothesisA3 and by showing that the maximal order 2k of the zeros off –m _f is the only parameter which characterizes the rate of convergence of ₁ ⁽ⁿ⁾ tom _f .     

A “Multiplicative Coboundary” theorem for some sequences of random matrices

Schmidt(¹⁰) showed that if the family of distributions of the partial sums of a strictly stationary random sequence is tight, then that random sequence is a coboundary. Here an analog of that result is proved for some sequences of random matrices, with partial sums replaced by matrix products.     

Spectral-Null Codes and Null Spaces of Hadamard Submatrices

Codes of length 2 ^m over {1, -1} are defined as null spaces of certain submatrices of Hadamard matrices. It is shown that the codewords of all have an rth order spectral null at zero frequency. Establishing the connection between and the parity-check matrix of Reed-Muller codes, the minimum distance of is obtained along with upper bounds on the redundancy of . An efficient algorithm is presented for encoding unconstrained binary sequences into .     

Automated molecular design: A new fragment-joining algorithm

Summary A popular first step in the problem of structure-based, de novo molecule design is to identify regions where specific functional groups or chemical entities would be expected to interact strongly. When the three-dimensional structure of the receptor is not available, it may be possible to derive a pharmacophore giving the three-dimensional relationships between such chemical groups. The task then is to design synthetically feasible molecules which not only contain the required groups, but which can also position them in the desired relative orientation. One way to do this is to first link the groups using an acyclic chain. We have investigated the application of the tweak algorithm [Shenkin, P.S. et al., Biopolymers, 26 (1987) 2053] for generating families of acyclic linkers. These linking structures can subsequently be braced using a ring-joining algorithm [Leach, A.R. and Lewis, R.A., J. Comput. Chem., 15 (1994) 233], giving rise to an even wider variety of molecular skeletons for further studies.     

Thermal degradation of polystyrene in the presence of hydrogen by catalyst in solution

For the first time, low temperature degradation (170-240 °C) of polystyrene in benzene is carried out in the presence of hydrogen using iron(III) oxide catalyst. The effect of temperature, catalyst loading and polymer loading on degradation are studied in hydrogen atmosphere. Degradation is also carried out at different initial hydrogen partial pressure. The time dependent molecular weight is calculated using viscosity average method. It is found that the degradation is enhanced considerably in the presence of hydrogen and followed random degradation chain scission. A random degradation kinetic model of Kelen [Kelen T. Polymer degradation. New York: Van Nostrand Reinhold Company; 1983.] is used to estimate the degradation rate constants. Empirical correlations are proposed to account for the effect of catalyst loading and initial hydrogen partial pressure on degradation. The true thermal degradation rate constants are calculated using these proposed correlations at given catalyst loading and initial hydrogen partial pressure with varying temperature. The frequency factor and activation energy are also determined using Arrhenius equation considering the true thermal degradation rate constants.     

Computation of suboptimal randomized strategies for steering the random motion of a point under partial observation

Consider the random motion in the plane of a pointM, whose velocityv=(v ₁,v ₂) is perturbed by an ²-valued Gaussian white noise. Only noisy nonlinear observations taken on the point location (state) are available toM. The velocityv is of the formv(y)= _u (u ₁,u ₂) _y (du), wherey denotes the value of the observed signal,U is the range of the velocity, and, for eachy, _y is a probability measure on (U). Using the available observations, the pointM wishes to steer itself into a given target set by choosing a randomized strategy ={ _y :y ²}. Sufficient conditions on weak optimal randomized strategies are derived. An algorithm for computing weak suboptimal randomized strategies is suggested, and the strategies are computed for a variety of cases.This work was partially supported by a grant from Control Data.     

Laponite clay in homopolymer and tri-block copolymer matrices

Macromolecule/laponite nanomaterials were studied by DSC and X-ray diffraction techniques. The matrices are poly(ethylene) glycols at various molecular masses and poly(ethylene oxides)-poly(propylene oxides)-poly(ethylene oxides) tri-block copolymers. The latter were tuned by modulating the molecular masses, at constant hydrophilic/hydrophobic ratio, and the hydrophilicity. For all the investigated systems, the enthalpy of melting (ΔH _m) is nearly constant up to a given composition thereafter it increases monotonically reaching the value of the pure macromolecule. We proposed a model to interpret the DSC data. Briefly, it was invoked a mechanism of interaction following which some segments of the adsorbed macromolecule are anchored to the laponite (RD) particles and the remaining segments are radiating away from the surface. The portion of the macromolecule in contact with RD does not contribute to ΔH _m whereas that radiating away from the clay does. Once that the RD surface is saturated, the excess of the macromolecule behaves like the pure one. The proposed model allowed to compute successfully the ΔH _m values. The X-ray diffraction experiments ruled out the polymer intercalation between the silicate sheets.     

Trapping of random walks on the line

Several features of the trapping of random walks on a one-dimensional lattice are analyzed. The results of this investigation are as follows: (1) The correction term to the known asymptotic form for the survival probability ton steps is O(( ₂n)^–1/3), where =–ln(1–c), andc is the trap concentration. (2) The short time form for the survival probability is found to be exp[–a(c)n ^1/2], wherea(c) is given in Eq. (21). (3) The mean-square displacement of a surviving random walker is found to go liken ^2/3for largen. (4) When the distribution of trap-free regions is changed so that very large regions are much rarer than for ideally random trap placement the asymptotic survival probability changes its dependence onn. One such model is studied.     

On the statistical independence of various column contributions to band broadening. Part 1: Second moment contributions from statistically independent,longitudinal diffusion in both phases

The total length-based second moment contribution from longitudinal sample diffusion in both phases on a column, σD , is derived by adding individual partial differential contributions to a partial differential equation accounting for the longitudinal diffusion processes only. Although each diffusion-dispersed sample part is equilibrated between two phases, the resulting σ,D (= 2D _mt _m + 2D _st _s) can be interpreted as the sum of two independent contributions in accordance with the variance addition rule. (D _m and D _s are the mean diffusion coefficients and t _mand t _s the mean residence times of the sample in the mobile and stationary phases, respectively.) The same σD expression is derived from the random walk model of Giddings by treating the diffusional process in each phase as statistically independent of the other processes. Under these conditions the broadening contribution from longitudinal diffusion in the mobile phase is shown to be independent of the velocity profile.