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Molecular Dynamics Simulations of a Ten-Amino Acid Protein
Athanasia P. Serafeim and Nicholas M. Glykos
Democritus University of Thrace, Health Sciences School, Department of Molecular Biology and Genetics
Introduction
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Mini-proteins play an important role in the study of protein folding. The well-defined
3D structure and two-state folding along with their small size qualify mini-proteins
as ideal to be studied using molecular dynamics simulations. In this study we
simulate the folding of CLN025, a synthetic molecule with the sequence
YYDPETGTWY that forms a beta hairpin as determined by X-ray crystallography
and NMR analyses[1]. With this work we aim to examine the agreement between the
available experimentally produced structures and the molecular dynamics structures
and to validate the force fields used in the simulations through this comparison.
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??.6FC71 86E51 ??.@6FC71 .D67,1 E5D1 B7D1 E59E1 67FCD1 E5D1 .6,,DE1 FED1 B1 2
BDE1 B7B9E6B7317BE5D1 6,76697E1 C6DD7D1 61 E59E1 671 E5D1 9D1 B1 ??.@
6FC71 97C1 ??.6FC71 E5DDA1 91 D,6B71 B1 56,51 >1 =9FD1 671 E5D1 FED1 B1 79E6=D1
EED1E59E1E5D1??.6FC7711F913
Methods
Molecular dynamics simulations were performed with the parallel molecular
dynamics code, NAMD[2] and the use of three force fields of the Amber family:
ff99sb-ildn, ff99sb-ildn-nmr, ff99sb*-ildn.
Results
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6DFC3
Conclusions & Future Work
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971FD9C1EB16,76697E1597,D1671E5D1%DC6EDC1BFC67,1.D59=6B1B1E5618DFFEC6DC1
%D%E6CD315D19=96F9.6F6E81B1D6ED76=D1D6%D6D7E9F1C9E91B1E5618ED15BFC19FFB81
1 EB1 B%9D1 97C1 =9F6C9ED1 E5D1 E5DD1 BD1 6DFC1 9,967E1 E5D1 981 D6%D6D7E9F1
!967F819:)$1C9E931A9=67,196C1E59E197C1.9DC1B71E5D1DFE15B871671<6,316E1
9%%D91E59E1D=D719E1E561D9F81E9,D1B1E5D1979F861E5D1??4*4)B5491=9697E1
%B6.F81 BE%DB1 E5D1 BE5D1 E8B1 =9697E1 .BE51 86E51 D%DE1 EB1 E5D1 %DC6EDC1
E5DBC87961 E9.6F6E81 B1E5D1 BFCDC1 E9ED1!FD1 B=DE9.6F629E6B71 B1 E5D1 %D%E6CDA1
79E6=D1E9ED$197C1E5D19,DDD7E186E51E5D179E6=DE9ED1EED1!56,5D1C=9FD$31
Figure 1: Amber ff99db*-ildn: Diagram presenting the similarity between the simulation and the
experimental structure (q) in a temperature range of 280K to 530K (T). Characteristic structures
are shown.
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References
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