Insertion of peptide chains into lipid membranes: An off‐lattice Monte Carlo dynamics model

  title={Insertion of peptide chains into lipid membranes: An off‐lattice Monte Carlo dynamics model},
  author={Mariusz Milik and Jeffrey Skolnick},
  journal={Proteins: Structure},
A combination of dynamic Monte Carlo simulation techniques with a hydropathy scale method for the prediction of the location of transmembrane fragments in membrane proteins is described. The new hydropathy scale proposed here is based on experimental data for the interactions of tripeptides with phospholipid membranes (Jacobs, R.E., White, S.H. Biochemistry 26:6127–6134, 1987) and the self‐solvation effect in protein systems (Roseman, M.A., J. Mol. Biol. 200:513–522, 1988). The simulations give… 

Modeling of Peptides in Implicit Membrane-Mimetic Media

The model is employed in non-restrained Monte Carlo simulations of several peptides: totally apolar 20-residue poly-L-Leu, hydrophobic peptide with polar edges, and strongly amphiphilic pep-tide to explore energy landscape and characterize the structures of low-energy states and their orientations with respect to the bilayer.

Modeling of peptides and proteins in a membrane environment: I. A solvation model mimicking a lipid bilayer

A theoretical solvation model of peptides and proteins that mimics the heterogeneous membrane-water system was proposed. Our approach is based on the combined use of atomic parameters of solvation

Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study.

  • P. HuangG. Loew
  • Biology, Chemistry
    Journal of biomolecular structure & dynamics
  • 1995
The hypothesis that the amphiphilic environment of a membrane surface is important in the induction of peptide amphiphilicity alpha-helical secondary structure is supported.

Implicit solvent simulations of peptide interactions with anionic lipid membranes

A recently developed implicit membrane model is supplemented with a Gouy–Chapman term describing counterion‐screened electrostatic interactions of a solute with negatively charged membrane lipids that opens the way to exploring the effect of membrane charge on the location, conformation, and dynamics of a large variety of biologically active peptides on membranes.

IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies

An empirical method to account for water–lipid interfaces in the insertion of molecules interacting with bilayers is presented and provides insights of the behaviors of the peptide dynamics that cannot be obtained with statistical approaches.

Insertion and Hairpin Formation of Membrane Proteins: A Monte Carlo Study

It is shown that in the absence of lipids the orientation of proteins is not stable and the formation of hairpins is absent and the insertion process follows a well-defined pattern of kinetic steps.



NMR studies of the structure and dynamics of membrane-bound bacteriophage Pf1 coat protein.

By comparing the structure and dynamics of the membrane-bound coat protein with that of the viral form as determined by NMR and neutron diffraction, essential features of assembly process can be identified.

The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices.

An interfacial hydrophobicity scale, IFH(h), with a variable hydrogen bond parameter (h), is introduced that permits one to consider explicitly hydrogen bonding in transbilayer helix searches.

Monte Carlo studies of an idealized model of a lipid-water system

Employing Monte Carlo dynamics, the equilibrium and dynamic properties of lipid-water systems are studied in the context of a diamond lattice realization. The model faithfully describe the lipid

A 'molten-globule' membrane-insertion intermediate of the pore-forming domain of colicin A

The variation of the kinetic constant of membrane insertion of the protein into negatively charged lipid vesicles as a function of the interfacial pH correlates with the appearance of the acidic molten globular state, indicating that this state could be an intermediate formed during the insertion of colicin A into membranes.

The structure of melittin in membranes.

Thermodynamics and kinetics of protein incorporation into membranes.

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    Proceedings of the National Academy of Sciences of the United States of America
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The free energy and enthalpy of protein incorporation into membranes are calculated with special emphasis on the hitherto neglected effects of immobilization of protein and perturbation of lipid

A critical evaluation of the hydropathy profile of membrane proteins.

New membrane-preference scales are introduced for categories of membrane proteins with different functions. A statistical analysis is carried out with several scales to verify the relative accuracy

Comparison of the conformation and orientation of alamethicin and melittin in lipid membranes.

  • H. Vogel
  • Chemistry, Biology
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It is shown that the commonly used set of CD spectra of water-soluble reference proteins is unsuitable to describe the CD specta of alamethicin correctly and therefore the secondary structure ofAlamethiin as derived from CD measurements is at the present state of analysis unreliable.

Primary structure and sidechain interactions of PFL filamentous bacterial virus coat protein

The first system for which a molecular model of a structural protein has been described in sufficient detail to permit study of the bonding specificity between proteins is described, finding that α helices are arranged in the virion so that hydrophobic sidechains on each protein subunit can fit into the space between sidechain on neighbouring subunits.