Abstract
The effect of terminal group charge on the structure and dynamics of the alanine tetrapeptide has been investigated using molecular dynamics simulations. Neutral and positive N-termini, together with neutral and negative C-termini, were studied, resulting in a total of four 10 ns simulations with different terminal group charge combinations. Analysis of these simulations indicates that the terminal group charge has only a minor effect on the conformations sampled for the central dihedrals, but a significant effect on the population distribution of the dihedrals close to the terminal groups. The conformational distribution at the C-terminus (ψ3) was also found to depend on the charge at the N-terminus. Here, the differences result from the formation of transient ion pairs (salt bridges) in the zwitterion case. However, equilibrium sampling of these intramolecular ion pairs was still not fully converged even after 10 ns.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 7628-7634 |
| Number of pages | 7 |
| Journal | Journal of Physical Chemistry B |
| Volume | 101 |
| Issue number | 38 |
| State | Published - Sep 18 1997 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Engineering(all)
Cite this
Protonation effects on the equilibrium and dynamical properties of the alanine tetrapeptide. / Blatt, Herb D.; Smith, Paul E.; Pettitt, Bernard.
In: Journal of Physical Chemistry B, Vol. 101, No. 38, 18.09.1997, p. 7628-7634.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Protonation effects on the equilibrium and dynamical properties of the alanine tetrapeptide
AU - Blatt, Herb D.
AU - Smith, Paul E.
AU - Pettitt, Bernard
PY - 1997/9/18
Y1 - 1997/9/18
N2 - The effect of terminal group charge on the structure and dynamics of the alanine tetrapeptide has been investigated using molecular dynamics simulations. Neutral and positive N-termini, together with neutral and negative C-termini, were studied, resulting in a total of four 10 ns simulations with different terminal group charge combinations. Analysis of these simulations indicates that the terminal group charge has only a minor effect on the conformations sampled for the central dihedrals, but a significant effect on the population distribution of the dihedrals close to the terminal groups. The conformational distribution at the C-terminus (ψ3) was also found to depend on the charge at the N-terminus. Here, the differences result from the formation of transient ion pairs (salt bridges) in the zwitterion case. However, equilibrium sampling of these intramolecular ion pairs was still not fully converged even after 10 ns.
AB - The effect of terminal group charge on the structure and dynamics of the alanine tetrapeptide has been investigated using molecular dynamics simulations. Neutral and positive N-termini, together with neutral and negative C-termini, were studied, resulting in a total of four 10 ns simulations with different terminal group charge combinations. Analysis of these simulations indicates that the terminal group charge has only a minor effect on the conformations sampled for the central dihedrals, but a significant effect on the population distribution of the dihedrals close to the terminal groups. The conformational distribution at the C-terminus (ψ3) was also found to depend on the charge at the N-terminus. Here, the differences result from the formation of transient ion pairs (salt bridges) in the zwitterion case. However, equilibrium sampling of these intramolecular ion pairs was still not fully converged even after 10 ns.
UR - http://www.scopus.com/inward/record.url?scp=0031232510&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0031232510&partnerID=8YFLogxK
M3 - Article
VL - 101
SP - 7628
EP - 7634
JO - Journal of Physical Chemistry B Materials
JF - Journal of Physical Chemistry B Materials
SN - 1520-6106
IS - 38
ER -