Dynamics of Alpha-Helix Formation in the CSAW Model

We study the folding dynamics of polyalanine (Ala$_{20}$), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain in Brownian motion, with interactions that include hydrophobic forces and internal hydrogen bonding. We find that large scale structures form before small scale structures, and obtain the relevant relaxation times. We find that helix nucleation occurs at two separate points on the protein chain. The evolution of small and large scale structures involve different mechanisms. While the former can be describe by rate equations governing the growth of helical content, the latter is akin to the relaxation of an elastic solid.Comment: 18 pages, 10 figure

The dynameomics entropy dictionary: a large-scale assessment of conformational entropy across protein fold space

YesMolecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing dataset of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identify deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, alpha-helices have lower entropy on average than do beta-sheets, and both are lower than coil regions.National Institutes of Health, US Department of Energy Office of Biological Research, National Energy Research Scientific Computing Center, Swedish Research Council, Knut and Alic Wallenberg Foundatio

Design of Force Fields from Data at Finite Temperature

We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs substantially from the ground state. We apply our method to systems modeling proteins and demonstrate that the correct potentials can be recovered even in the presence of thermal noise.Comment: 10 pages, 1 postcript figure, Late

Protein dynamics with off-lattice Monte Carlo moves

A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte Carlo moves are used: single rotations about torsion axes, and cooperative rotations in windows of amide planes, changing the conformation globally and locally, respectively. For local moves Jacobians are used to obtain an unbiased distribution of dihedrals. A molecular dynamics energy function adapted to the protein model is employed. A polypeptide is folded into native-like structures by local but not by global moves.Comment: 10 pages, 4 Postscript figures, uses epsf.sty and a4.sty; scheduled tentatively for Phys.Rev.E issue of 1 March 199

Anatomic and histological study of the anterolateral aspect of the knee: a SANTI Group investigation

Background: The structure and function of the anterolateral aspect of the knee have been significantly debated, with renewed interest in this topic since the description of the anterolateral ligament (ALL). Purpose: To define and describe the distinct structures of the lateral knee and to correlate the macroscopic and histologic anatomic features. Study Design: Descriptive laboratory study. Methods: Twelve fresh-frozen human cadavers were used for anatomic analysis. In the left knee, a layer-by-layer dissection and macroscopic analysis were performed. In the right knee, an en bloc specimen was obtained encompassing an area from the Gerdy tubercle to the posterior fibular head and extending proximally from the anterior aspect to the posterior aspect of the lateral femoral epicondyle. The en bloc resection was then frozen, sliced at the level of the joint line, and reviewed by a musculoskeletal pathologist. Results: Macroscopically, the lateral knee has 4 main layers overlying the capsule of the knee: the aponeurotic layer, the superficial layer including the iliotibial band (ITB), the deep fascial layer, and the ALL. Histologically, 8 of 12 specimens demonstrated 4 consistent, distinct structures: the ITB, the ALL, the lateral collateral ligament, and the meniscus. Conclusion: The lateral knee has a complex orientation of layers and fibers. The ALL is a distinct structure from the ITB and is synonymous to the previously described capsulo-osseous layer of the ITB. Clinical Relevance: Increasingly, lateral extra-articular procedures are performed at the time of anterior cruciate ligament reconstruction. Understanding the anatomic features of the anterolateral aspect of the knee is necessary to understand the biomechanics and function of the structures present and allows surgeons to attempt to replicate those anatomic characteristics when performing extra-articular reconstruction

Perspectives on Andean Prehistory and Protohistory: Papers from the Third Annual Northeast Conference on Andean Archaeology and Ethnohistory

This volume represents eight of the eighteen papers presented at the Third Northeast Conference on Andean Archaeology and Ethnohistory held at the University of Massachusetts, Amherst on October 27 and 28, 1984. It also includes a paper presented at the Second NCAAE held at the American Museum of Natural History on November 19-20, 1983. The papers include: Wandering Shellfish: New Insights from Southeastern Coastal Ecuador by Patricia Netherly, Late Prehistoric Terracing at Chijra in the Collca Valley, Peru: Preliminary Report I by Michael A. Malpass, The Topara Tradition: An Overview by Dwight T. Wallace, The Peruvian North Central Coast During the Early Intermediate Period: An Emerging Perspective by Richard E. Daggett, A Sequence of Monumental Architecture from Huamanchuco by John R. Topic, Duality in Public Architecture in the Upper Zena Valley by Patricia J. Netherly and Tom D. Dillehay, Piruru: A Preliminary Report on the Archaeological Botany of a Highland Andean Site by Lawrence Kaplan and Elisabeth Bonnier, Analysis of Organic Remains from Huamachuco Qollqas by Coreen E. Chiswell, Aspects of Casting Practice in Prehispanic Peru by Stuart V. Arnold, and Representations of the Cosmos: A Comparison of the Church of San Cristobal de Pampachiri with the Coricancha Drawing of Santacruz Pachacuti Yamqui Salcamaygua by Monica Barnes.https://digitalcommons.library.umaine.edu/andean_past_special/1000/thumbnail.jp

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation

Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Unfolding Simulations of Holomyoglobin from Four Mammals: Identification of Intermediates and β-Sheet Formation from Partially Unfolded States

Myoglobin (Mb) is a centrally important, widely studied mammalian protein. While much work has investigated multi-step unfolding of apoMb using acid or denaturant, holomyoglobin unfolding is poorly understood despite its biological relevance. We present here the first systematic unfolding simulations of holoMb and the first comparative study of unfolding of protein orthologs from different species (sperm whale, pig, horse, and harbor seal). We also provide new interpretations of experimental mean molecular ellipticities of myoglobin intermediates, notably correcting for random coil and number of helices in intermediates. The simulated holoproteins at 310 K displayed structures and dynamics in agreement with crystal structures (R g ~1.48-1.51 nm, helicity ~75%). At 400 K, heme was not lost, but some helix loss was observed in pig and horse, suggesting that these helices are less stable in terrestrial species. At 500 K, heme was lost within 1.0-3.7 ns. All four proteins displayed exponentially decaying helix structure within 20 ns. The C- and F-helices were lost quickly in all cases. Heme delayed helix loss, and sperm whale myoglobin exhibited highest retention of heme and D/E helices. Persistence of conformation (RMSD), secondary structure, and ellipticity between 2-11 ns was interpreted as intermediates of holoMb unfolding in all four species. The intermediates resemble those of apoMb notably in A and H helices, but differ substantially in the D-, E- and F-helices, which interact with heme. The identified mechanisms cast light on the role of metal/cofactor in poorly understood holoMb unfolding. We also observed β-sheet formation of several myoglobins at 500 K as seen experimentally, occurring after disruption of helices to a partially unfolded, globally disordered state; heme reduced this tendency and sperm-whale did not display any sheet propensity during the simulations