Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints

Summary A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985)J. Mol. Biol.,186, 611) is described, which makes use of redundant dihedral angle constraints (REDAC) derived from preliminary calculations of the complete structure. The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space.Dedicated to the memory of Professor V.F. Bystrov     

The multiple-minima problem in the conformational analysis of polypeptides. III. An Electrostatically Driven Monte Carlo Method: Tests on enkephalin

The three-dimensional conformation of Met-enkephalin, corresponding to the lowest minimum of the empirical potential energy function ECEPP/2 (empirical conformational energy program for peptides), has been determined using a new algorithm, viz. the Electrostatically Driven Monte Carlo Method. This methodology assumes that a polypeptide or protein molecule is driven toward the native structure by the combined action of electrostatic interactions and stochastic conformational changes associated with thermal movements. These features are included in the algorithm that produces a Monte Carlo search in the conformational hyperspace of the polypeptide, using electrostatic predictions and a random sampling technique to locate low-energy conformations. In addition, we have incorporated an alternative mechanism that allows the structure to escape from some conformational regions representing metastable local energy minima and even from regions of the conformational space with great stability. In 33 test calculations on Met-enkephalin, starting from arbitrary or completely random conformations, the structure corresponding to the global energy minimum was found inall the cases analyzed, with a relatively small search of the conformational space. Some of these starting conformations wereright orleft-handed -helices, characterized by good electrostatic interactions involving their backbone peptide dipoles; nevertheless, the procedure was able to convert such locally stable structures to the global-minimum conformation.On leave from the National University of San Luis, Faculty of Sciences and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Matemática Aplicada, San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina.     

Prediction of Individual Muscle Forces Using Lagrange Multipliers Method — A Model of the Upper Human Limb in the Sagittal Plane: II. Numerical Experiments and Sensitivity Analysis

Abstract

Using the method of Lagrange multipliers an analytical solution of the optimization problem formulated for a two-dimensional, 3DOF model of the human upper limb has been described in Part I of this investigation. The objective criterion used is the following: Σ c_iF_i ², where F_i-s are the muscle forces modelled and c_i-s are unknown weight factors. This study is devoted to the numerical experiments performed in order to investigate which sets of the weight factors may predict physiologically reasonable muscle forces and joint reactions. A sensitivity analysis is also presented. The influence of: the gravity forces, different external loads applied to the hand, changes of the weight factors and of joint angle on the optimal solution is studied. A general conclusion may be drawn: using the above mentioned objective criterion, practically all motor tasks performed by the human upper limb may be described if the c_i-s are properly chosen. These weight factors generally depend on the joint moments and must be different (their magnitudes as well as their signs) for agonistic muscles and for their antagonists.     

Pair formation models with maturation period

The standard model for pair formation is generalized to include a maturation period. This model in the form of three coupled delay equations is a special case of the general age-structured model for a two-sex population. The exact conditions for the existence of an exponential (persistent) two-sex solution are derived. It is shown that this solution is unique and locally stable. In order to achieve these results the theory of homogeneous differential equations is extended to a class of homogeneous delay equations.     

Vervet monkeys use paths consistent with context‐specific spatial movement heuristics

Animal foraging routes are analogous to the computationally demanding “traveling salesman problem” (TSP), where individuals must find the shortest path among several locations before returning to the start. Humans approximate solutions to TSPs using simple heuristics or “rules of thumb,” but our knowledge of how other animals solve multidestination routing problems is incomplete. Most nonhuman primate species have shown limited ability to route plan. However, captive vervets were shown to solve a TSP for six sites. These results were consistent with either planning three steps ahead or a risk‐avoidance strategy. I investigated how wild vervet monkeys (Chlorocebus pygerythrus) solved a path problem with six, equally rewarding food sites; where site arrangement allowed assessment of whether vervets found the shortest route and/or used paths consistent with one of three simple heuristics to navigate. Single vervets took the shortest possible path in fewer than half of the trials, usually in ways consistent with the most efficient heuristic (the convex hull). When in competition, vervets' paths were consistent with different, more efficient heuristics dependent on their dominance rank (a cluster strategy for dominants and the nearest neighbor rule for subordinates). These results suggest that, like humans, vervets may solve multidestination routing problems by applying simple, adaptive, context‐specific “rules of thumb.” The heuristics that were consistent with vervet paths in this study are the same as some of those asserted to be used by humans. These spatial movement strategies may have common evolutionary roots and be part of a universal mental navigational toolkit. Alternatively, they may have emerged through convergent evolution as the optimal way to solve multidestination routing problems.