| Literature DB >> 26114384 |
Zanxia Cao1,2, Xiumei Zhang3,4, Lei Liu5, Liling Zhao6,7, Haiyan Li8,9, Jihua Wang10,11.
Abstract
The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6-Asp2 contact may prevent the dimerization.Entities:
Keywords: different pH; dimerization; molecular dynamics simulation; structural character; α-synuclein
Mesh:
Substances:
Year: 2015 PMID: 26114384 PMCID: PMC4519842 DOI: 10.3390/ijms160714291
Source DB: PubMed Journal: Int J Mol Sci ISSN: 1422-0067 Impact factor: 5.923
Figure 1Free energy surface (in kJ/mol) of the (α-syn12)2 dimer (A) at the physiological pH and (B) at the acidic pH projected on the first two principal components PC1 and PC2 obtained from PCA of inter-chain side-chain inverse distances. The blue indicates the N-terminal.
The relative depths of the free energy minima of the α-syn12 dimer at the physiological pH.
| The Different Regions | The Relative Depths (kJ mol−1) of the Minima at Physiology pH |
|---|---|
| 201–500 ns | |
| A | 0 |
| B | 2.5 |
| C | 3.6 |
| D | 0.1 |
| E | 1.8 |
| F | 4.1 |
Figure 2The free energy surface (in kJ/mol) of the (α-syn12)2 dimer projected on other representative reaction coordinates. (A) is the free energy surface based on the X-axis and the number of side chain contact at physiological pH; (B) is the free energy surface based on the X-axis and the number of side chain contact at acidic pH; (C) is the free energy surface based on the number of side chain contact and the number of intermolecular hydrogen bond at physiological pH; and (D) is the free energy surface based on the number of side chain contact and the number of intermolecular hydrogen bond at acidic pH The X-axis represents the existence of the following: (VI), NUMintraHB > 0, Lhelix > 0, Lsheet = 0; (V), NUMintraHB > 0, Lhelix > 0, Lsheet > 0; (IV), NUMintraHB > 0, Lhelix = 0, Lsheet = 0; (III), NUMintraHB > 0, Lhelix = 0, Lsheet > 0; (II), NUMintraHB = 0, Lhelix = 0, Lsheet > 0; and (I), NUMintraHB = 0, Lhelix = 0, Lsheet = 0.
The relative depths of the free energy minima of the α-syn12 dimer at the acidic pH.
| The Different Regions | The Relative Depths (kJ mol−1) of the Minima at Acidic pH |
|---|---|
| 201–500 ns | |
| A' | 0 |
| B' | 1.1 |
| C' | −0.6 |
| D' | 6.1 |
The respective probabilities for the α-syn12 dimer fall within different inter-backbone hydrogen bonds at the different pH and simulation time. The results at the acidic pH are shown in the brackets.
| The Different Regions | 1–100 ns | 101–200 ns | 201–300 ns | 301–400 ns | 401–500 ns |
|---|---|---|---|---|---|
| NUMinterHB = 0 | 0.18 (0.14) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| NUMinterHB > 0, 0° ≤ θ ≤ 50° | 0.28 (0.03) | 0.15 (0) | 0.10 (0) | 0.10 (0) | 0.07 (0) |
| NUMinterHB > 0, 50° ≤ θ ≤ 90° | 0.27 (0.24) | 0.14 (0.22) | 0.17 (0.25) | 0.10 (0.29) | 0.09 (0.20) |
| NUMinterHB > 0, 90° < θ < 130° | 0.15 (0.23) | 0.18 (0.20) | 0.13 (0.21) | 0.18 (0.22) | 0.12 (0.25) |
| NUMinterHB > 0, 130° ≤ θ ≤ 180° | 0.12 (0.23) | 0.53 (0.42) | 0.59 (0.41) | 0.62 (0.38) | 0.72 (0.45) |
Figure 3The free energy surfaces (in kJ/mol) for A–F regions of the (α-syn12)2 dimer at the physiological pH and A'–D' regions at the acidic pH projected on the number of intra-backbone hydrogen bonds and the number of inter-backbone hydrogen bonds.
Figure 4The possible transformation pathways.
Figure 5The initial structure of (α-syn12)2 used in the T-REMD simulation.
The respective probabilities for the α-syn12 dimer fall within different regions at the different pH values and simulation times. The results at the acidic pH are shown in the brackets.
| The Different Regions | 1–100 ns | 101–200 ns | 201–300 ns | 301–400 ns | 401–500 ns |
|---|---|---|---|---|---|
| NUMintraHB > 0, Lhelix > 0, Lsheet = 0; Cited as VI | 0.23 (0.11) | 0.04 (0) | 0 (0) | 0 (0) | 0 (0) |
| NUMintraHB > 0, Lhelix > 0, Lsheet > 0; Cited as V | 0.17 (0.04) | 0.04 (0) | 0 (0) | 0 (0) | 0 (0) |
| NUMintraHB > 0, Lhelix = 0, Lsheet = 0; Cited as IV | 0.04 (0.04) | 0.01 (0.01) | 0 (0.03) | 0 (0) | 0 (0.01) |
| NUMintraHB > 0, Lhelix = 0, Lsheet > 0; Cited as III | 0.48 (0.69) | 0.37 (0.54) | 0.32 (0.39) | 0.23 (0.41) | 0.16 (0.41) |
| NUMintraHB = 0, Lhelix > 0, Lsheet = 0 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| NUMintraHB = 0, Lhelix > 0, Lsheet > 0 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| NUMintraHB = 0, Lhelix = 0, Lsheet > 0; Cited as II | 0.07 (0.10) | 0.53 (0.40) | 0.67 (0.48) | 0.75 (0.49) | 0.82 (0.49) |
| NUMintraHB = 0, Lhelix = 0, Lsheet = 0; Cited as I | 0 (0.02) | 0 (0.04) | 0 (0.09) | 0 (0.09) | 0.01 (0.08) |
The respective probabilities for the α-syn12 dimer fall within the different regions (from VI to I) at the different pH and simulation time. The results at acidic pH are shown in the brackets.
| The Different Regions | 1–100 ns | 101–200 ns | 201–300 ns | 301–400 ns | 401–500 ns |
|---|---|---|---|---|---|
| VI and NUMcon > 0 | 0.20 (0.06) | 0.04 (0) | 0 (0) | 0 (0) | 0 (0) |
| VI and NUMcon = 0 | 0.04 (0.05) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| V and NUMcon > 0 | 0.17 (0.03) | 0.04 (0) | 0 (0) | 0 (0) | 0 (0) |
| V and NUMcon = 0 | 0 (0.01) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| IV and NUMcon > 0 | 0.04 (0.04) | 0.01 (0.01) | 0 (0.03) | 0 (0) | 0 (0.01) |
| IV and NUMcon = 0 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| III and NUMcon > 0 | 0.48 (0.64) | 0.37 (0.54) | 0.32 (0.39) | 0.23 (0.41) | 0.16 (0.41) |
| III and NUMcon = 0 | 0 (0.05) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| II and NUMcon > 0 | 0.07 (0.10) | 0.53 (0.40) | 0.67 (0.48) | 0.75 (0.49) | 0.82 (0.49) |
| II and NUMcon = 0 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| I and NUMcon > 0 | 0 (0.02) | 0 (0.04) | 0 (0.09) | 0 (0.09) | 0.01 (0.08) |
| I and NUMcon = 0 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |