62,748 research outputs found
Geometrical approach to protein folding: a tube picture
No full textA framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed characteristics of protein structures. The authors show here that proteins may be regarded as tubes of nonzero thickness. This approach allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. The continuum description of a tube (or a sheet) of arbitrary thickness entails using appropriately chosen many-body interactions rather than two-body interactions. The authors suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. This approach also offers an explanation for why helices and sheets are the building blocks of protein structures
Monte-carlo Mean-field Theory
No full textA Comment on the Letter by R. R. Netz and A. N. Berker, Phys. Rev. Lett. 66, 377 (1991)
Spin-flip Avalanches and Dynamics of 1st-order Phase-transitions
No full textA Comment on the Letter by J. P. Sethna et al., Phys. Rev. Lett. 70, 3347 (1993)
The Science of Life
No full textThe advent of powerful computers and algorithms
combined with new, powerful ways of thinking about
problems in statistical physics has created an unprecedented
opportunity for making significant breakthroughs
in a variety of interdisciplinary problems,
most notably in the life sciences
Chaos, Noise, and Synchronization - Reply
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Chaos, Noise, and Synchronization
No full textWe show that a pair of chaotic systems subjected to the same noise may undergo a transition at large enough noise amplitude and follow almost identical trajectories with complete insensitivity to initial conditions. An analytic argument is presented to show that a pair of generic systems in the same potential evolving to equilibrium through standard Langevin dynamics with the same noise collapse into the same trajectory at long times
Comment on the protein folds as platonic forms
No full textDenton et al. (2002) have presented compelling evidence that protein folds ought to be understood as arising from physical laws rather than natural selection. Furthermore, they suggest this could have “implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form.” They do not, however, explain what the physical basis is for understanding the origin of protein folds. Here, we wish to address this key missing ingredient
Scoring functions in protein folding and design
No full textWe present an analysis of the assumptions behind some of the most commonly used methods for evaluating the goodness of the fit between a sequence and a structure. Our studies on a lattice model show that methods based on statistical considerations are easy to use and can capture some of the features of protein-like sequences and their corresponding native states, but unfortunately are incapable of recognizing, with certainty, the native-like conformation of a sequence among a set of decoys. Meanwhile, an optimization method, entailing the determination of the parameters of an effective free energy of interaction, is much more reliable in recognizing the native state of a sequence. However, the statistical method is shown to perform quite well in tests of protein design
A comparative study of existing and new deign techniques for protein models
No full textWe present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The efficiency of design techniques is assessed as a function of protein length and the number of classes into which amino acids are coarse grained. It turns out that, while energy minimization strategies can identify correct solutions in most circumstances, it may be impossible for numerical implementations of design algorithms to meet the efficiency required to yield correct solutions in realistic contexts. Alternative design strategies based on an approximate treatment of the free energy are shown to be much more efficient than energy-based methods while requiring nearly the same CPU time. Finally, we present a novel iterative design strategy that incorporates negative design with the use of selected decoy structures that compete significantly with the target native state in housing the designed sequences. This procedure allows one to identify systematically all sequences that fold on a given target structure
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