𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Molecular dynamics simulations of β-hairpin folding

✍ Scribed by Hongwu Wang; Judith Varady; Lily Ng; Shen-Shu Sung

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
252 KB
Volume
37
Category
Article
ISSN
0887-3585

No coin nor oath required. For personal study only.

✦ Synopsis

Molecular dynamics simulations of ␤-hairpin folding have been carried out with a solvent-referenced potential at 274 K. The model peptide V 4 D PGV 4 formed stable ␤-hairpin conformations and the ␤-hairpin ratio calculated by the DSSP algorithm was about 56% in the 50-ns simulation. Folding into ␤-hairpin conformations is independent of the initial conformations. The simulations provided insights into the folding mechanism. The hydrogen bond often formed in a ␤-turn first, and then propagated by forming more hydrogen bonds along the strands. Unfolding and refolding occurred repeatedly during the simulations. Both the hydrogen bonding and the hydrophobic interaction played important roles in forming the ordered structure. Without the hydrophobic effect, stable ␤-hairpin conformations did not form in the simulations. With the same energy functions, the alanine-based peptide (AAQAA) 3 Y folded into helical conformations, in agreement with experiments. Folding into an ␣-helix or a ␤-hairpin is amino acid sequencedependent.

📜 SIMILAR VOLUMES

Effects of turn residues on β-hairpin fo
Effects of turn residues on β-hairpin folding—A molecular dynamics study
✍ Hongwu Wang; Shen-Shu Sung 📂 Article 📅 1999 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 258 KB

Folding of beta-hairpin structures of synthetic peptides has been simulated using the molecular dynamics method with a solvent-referenced potential. Two similar sequences, Ac-MQIFVKS(D)PGKTITLKV-NH(2) and Ac-MQIFVKS(L)PGKTITLKV-NH(2), derived from the N-terminal beta-hairpin of ubiquitin, were used

Computer simulations of protein folding
Computer simulations of protein folding by targeted molecular dynamics
✍ Philippe Ferrara; Joannis Apostolakis; Amedeo Caflisch 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 362 KB 👁 1 views

We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotrypsin inhibitor 2 (CI2) with an implicit solvation model for a total simulation time of 0.4 microseconds. Folding requires that the three-dimensional structure of the native state is known. It was simulated at 300 K by

Molecular dynamics simulations of xDNA
Molecular dynamics simulations of xDNA
✍ Mathew K. Varghese; Renjith Thomas; N. V. Unnikrishnan; C. Sudarsanakumar 📂 Article 📅 2009 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 394 KB
Molecular dynamics simulations of helix
Molecular dynamics simulations of helix folding: The effects of amino acid substitution
✍ Shen-Shu Sung; Xiong-Wu Wu 📂 Article 📅 1997 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 168 KB 👁 2 views

Molecular dynamics simulations were applied to helix folding of alanine-based synthetic peptides. A single alanine residue in the middle of the peptide was substituted with various nonpolar amino acids (leucine, isoleucine, valine, glycine, or proline) to study the effect of the substitution. Unlike

Molecular dynamics simulations of biomem
Molecular dynamics simulations of biomembrane models
✍ G. Vergoten 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 119 KB 👁 2 views

A molecular force field dedicated to molecular dynamics simulation of biomembranes was developed. It was parameterized on model compounds related to phospholipids and was able to reproduce at the same time structures, energies, and vibrational spectra. Cross terms in the potential energy function we

Explicit and implicit water simulations
Explicit and implicit water simulations of a β-hairpin peptide
✍ Buyong Ma; Ruth Nussinov 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 460 KB

The conformational properties of a ␤-hairpin peptide (YITNSDGTWT) were studied by using both explicit and implicit water simulations. The conformational space of the peptide was scanned by using a restricted hydrogen-bonding search method. The search method used generated the conformational space wi