Prem P Chapagain

Summary

Affiliation: Florida International University
Country: USA

Publications

  1. pmc Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry
    Prem P Chapagain
    Department of Physics, Florida International University, Miami, Florida 33199, USA
    J Chem Phys 135:235101. 2011
  2. ncbi request reprint Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories
    Prem P Chapagain
    Department of Physics, Florida International University, Miami, Florida 33199, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 83:061905. 2011
  3. ncbi request reprint Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 127:075103. 2007
  4. doi request reprint The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 129:175103. 2008
  5. doi request reprint Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper
    Yanxin Liu
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 128:045106. 2008
  6. ncbi request reprint Self-organization in protein folding and the hydrophobic interaction
    Bernard S Gerstman
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 123:054901. 2005
  7. pmc Exploring the diffusion of molecular oxygen in the red fluorescent protein mCherry using explicit oxygen molecular dynamics simulations
    Chola K Regmi
    Department of Physics, Florida International University, Miami, Florida 33199, United States
    J Phys Chem B 117:2247-53. 2013
  8. doi request reprint Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization
    Yuba R Bhandari
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 137:105103. 2012
  9. doi request reprint Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation
    Bernard S Gerstman
    Department of Physics, Florida International University, Miami, FL, USA
    Methods Mol Biol 932:191-204. 2013
  10. ncbi request reprint Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, FL 33199, USA
    Biopolymers 81:167-78. 2006

Collaborators

  • Bernard S Gerstman
  • Yuba R Bhandari
  • Yanxin Liu
  • Chola K Regmi
  • Ilan E Chemmama
  • Timothy Steckmann
  • Adam Colt Pelea
  • Zubair Awan
  • Jose L Parra

Detail Information

Publications14

  1. pmc Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry
    Prem P Chapagain
    Department of Physics, Florida International University, Miami, Florida 33199, USA
    J Chem Phys 135:235101. 2011
    ..We also show that these pathways can be blocked or altered and barrel fluctuations can be reduced by strategic amino acid substitutions...
  2. ncbi request reprint Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories
    Prem P Chapagain
    Department of Physics, Florida International University, Miami, Florida 33199, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 83:061905. 2011
    ..Transition pathways that involve intermediate configurations between two stable regions are allowed in this treatment, and therefore the results are valid for multistate systems...
  3. ncbi request reprint Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 127:075103. 2007
    ..We also discuss the problems that arise in attempting to count the huge number of individual states of the random coil at the top of the funnel...
  4. doi request reprint The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 129:175103. 2008
    ..We also find that a stronger trigger sequence not only increases the probability for dimerization but also changes the dimerization dynamics by introducing multiple intermediate states...
  5. doi request reprint Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper
    Yanxin Liu
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 128:045106. 2008
    ..Free energy landscapes and median first passage times for the folding process are calculated and elucidate experimentally measured characteristics such as the multistate nature of the dimerization process...
  6. ncbi request reprint Self-organization in protein folding and the hydrophobic interaction
    Bernard S Gerstman
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 123:054901. 2005
    ....
  7. pmc Exploring the diffusion of molecular oxygen in the red fluorescent protein mCherry using explicit oxygen molecular dynamics simulations
    Chola K Regmi
    Department of Physics, Florida International University, Miami, Florida 33199, United States
    J Phys Chem B 117:2247-53. 2013
    ..The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins...
  8. doi request reprint Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization
    Yuba R Bhandari
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 137:105103. 2012
    ..The results on folding and dimer stability provide important insights for designing proteins that involve trigger sites...
  9. doi request reprint Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation
    Bernard S Gerstman
    Department of Physics, Florida International University, Miami, FL, USA
    Methods Mol Biol 932:191-204. 2013
    ..We also show how amino acid sequences can be engineered by specific substitutions to optimize the folding to the desired supersecondary structure...
  10. ncbi request reprint Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, FL 33199, USA
    Biopolymers 81:167-78. 2006
    ..These results support arguments that removal of kinetic traps, obligatory or nonobligatory, is crucial for fast folding...
  11. doi request reprint Stabilization of native and non-native structures by salt bridges in a lattice model of the GCN4 leucine dimer
    Yanxin Liu
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Phys Chem B 114:796-803. 2010
    ..These structures may be relevant to interesting recent experiments that have provided evidence of unusual forms of the leucine zipper GCN4-p1 called the LZ(GCN4) x-forms, which dominate the population in certain biochemical conditions...
  12. ncbi request reprint Excluded volume entropic effects on protein unfolding times and intermediary stability
    Prem P Chapagain
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    J Chem Phys 120:2475-81. 2004
    ..We find that entropic excluded volume effects are crucially important for stabilizing the organized native state relative to the molten globule...
  13. ncbi request reprint Structural propensities and entropy effects in peptide helix-coil transitions
    Ilan E Chemmama
    Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 86:031915. 2012
    ....
  14. ncbi request reprint Kinetics of peptide secondary structure conversion during amyloid β-protein fibrillogenesis
    Timothy Steckmann
    Theoretical and Computational Biophysics Group, Department of Physics, Florida International University, Miami, FL 33199, USA
    J Theor Biol 301:95-102. 2012
    ..The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process...