@article{marchut_hall_2007, title={Effects of chain length on the aggregation of model polyglutamine peptides: Molecular dynamics simulations}, volume={66}, ISSN={["0887-3585"]}, DOI={10.1002/prot.21132}, abstractNote={Abstract}, number={1}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Marchut, Alexander J. and Hall, Carol K.}, year={2007}, month={Jan}, pages={96–109} }
 @article{marchut_smith_hall_2006, title={Commentary on: "Assembly of a tetrameric alpha-helical bundle: Computer simulations on an intermediate-resolution protein model" [Proteins 2001;44 : 376-391]}, volume={63}, ISSN={["1097-0134"]}, DOI={10.1002/prot.20896}, abstractNote={The work of Smith and Hall is a computational study of the folding of an isolated model peptide and the assembly of four of the same model peptides into a four-helix bundle using an intermediate resolution protein model. Smith and Hall performed a total of 129 simulations on the isolated peptide and 50 simulations on the four-peptide system, starting from random configurations of random coils. They found that these systems frequently folded to their native states, an -helix in the case of the isolated peptide and a tetrameric -helical bundle in the case of the four-peptide system, if the simulation temperature was within an optimal temperature range. We found two errors in the computer code used to generate these results; these errors led to an underestimation of the frequency of amorphous aggregation of the peptides relative to folding into the native states. The first error occurred when the system velocities were rescaled to conserve energy after a hydrogen bond was dissolved because the angular restrictions on the hydrogen bond were no longer satisfied. In that case, the amount of energy to be removed by rescaling the system velocities was stored as an integer variable rather than as a real variable, causing this number to be rounded down to the nearest integer. This meant that the system gained too much kinetic energy after a hydrogen bond dissolved, because the angular restrictions were not satisfied. The second error occurred when the angular restrictions on the hydrogen bonds were checked. The periodic boundary conditions were not applied to the interaction that was being checked as they should have been. This meant that hydrogen bonds that should have formed across a periodic boundary did not form. Since intramolecular interactions never straddled the periodic boundary, because the box was sufficiently large, this error affected only intermolecular interactions, causing fewer intermolecular hydrogen bonds to form than should have. The formation of intramolecular hydrogen bonds was unaffected. Since the native state of the tetrameric -helical bundle has 48 intramolecular hydrogen bonds and no intermolecular hydrogen bonds, the bundle structure formed more frequently than it should have. This commentary reports the corrected results and an explanation of the effects that the computational errors had on the self-assembly of the model peptides. More simulations were performed than in the original article; 11 independent simulations were performed at each state point (for a total of 440 simulations) for the isolated peptide and 20 independent simulations were performed at each state point (for a total of 160 simulations) for the four-peptide case. The corrected version of the results presented in Figure 4 of Smith and Hall, which depicts the results of the isolated peptide simulations, is presented in Figure 1. The corrected version of the results presented in Figure 9 of Smith and Hall, which depicts the folding curve for the four-peptide system, is presented in Figure 2. Correcting the error associated with rescaling the system velocities after a hydrogen bond was dissolved due to the angular constraints resulted in an increase in kinetic trapping. For this reason the folding curve in Figure 1 is not as smooth as the folding curve in Figure 4 of Smith and Hall. When the error was present, the peptides were likely to unfold rapidly via a chain reaction in which the dissolution of one hydrogen bond caused the system to have too much kinetic energy, which then led to more hydrogen bonds breaking and more excess kinetic energy, and so on. In other words, this error caused the peptides to unfold more frequently than they should have, allowing them to sample additional configurational space and making it easier to avoid kinetic traps. The error associated with not applying the periodic boundary condition when checking the angular constraints on the hydrogen bonds strongly affected the four-peptide system. The isolated peptide simulations were unaffected by this error, since isolated peptides can only have intramolecular hydrogen bonds. The nativeness parameter, a measure of the structure of the four-helix bundle presented in Figure 2, is much lower than the nativeness parameter in Figure 9 of Smith and}, number={3}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Marchut, AJ and Smith, AV and Hall, CK}, year={2006}, month={May}, pages={709–710} }
 @article{marchut_hall_2006, title={Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations}, volume={90}, ISSN={["1542-0086"]}, DOI={10.1529/biophysj.105.079269}, abstractNote={The pathological manifestation of nine hereditary neurodegenerative diseases is the presence within the brain of aggregates of disease-specific proteins that contain polyglutamine tracts longer than a critical length. To improve our understanding of the processes by which polyglutamine-containing proteins misfold and aggregate, we have conducted molecular dynamics simulations of the aggregation of model polyglutamine peptides. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms, depending on the residue being modeled. The effects of hydrophobicity on the system are studied by varying the strength of the hydrophobic interaction from 12.5% to 5% of the hydrogen-bonding interaction strength. In our simulations, we observe the spontaneous formation of aggregates and annular structures that are made up of beta-sheets starting from random configurations of random coils. This result was interesting because tubular protofibrils were recently found in experiments on polyglutamine aggregation and because of Perutz's prediction that polyglutamine would form water-filled nanotubes.}, number={12}, journal={BIOPHYSICAL JOURNAL}, author={Marchut, Alexander J. and Hall, Carol K.}, year={2006}, month={Jun}, pages={4574–4584} }
 @article{marchut_hall_2006, title={Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides}, volume={30}, ISSN={["1476-928X"]}, DOI={10.1016/j.compbiolchem.2006.01.003}, abstractNote={Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglutamine chains 16 residues long at a concentration of 5 mM spontaneously formed large beta sheets which curved to form tube-like annular structures that resemble beta barrels. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms depending on the residue being modeled. Our results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglutamine forms water filled nanotubes.}, number={3}, journal={COMPUTATIONAL BIOLOGY AND CHEMISTRY}, author={Marchut, Alexander J. and Hall, Carol K.}, year={2006}, month={Jun}, pages={215–218} }
 @article{nguyen_marchut_hall_2004, title={Solvent effects on the conformational transition of a model polyalanine peptide}, volume={13}, ISSN={0961-8368}, url={http://dx.doi.org/10.1110/ps.04701304}, DOI={10.1110/ps.04701304}, abstractNote={Abstract}, number={11}, journal={Protein Science}, publisher={Wiley}, author={Nguyen, Hung D. and Marchut, Alexander J. and Hall, Carol K.}, year={2004}, month={Dec}, pages={2909–2924} }