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A Fragment Based Step-by-Step Strategy for Determining the Most Stable Conformers of Biomolecules
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.
University of Science and Technology of China.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, China.ORCID iD: 0000-0003-0007-0394
2014 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 610, 303-309 p.Article in journal (Refereed) Published
Abstract [en]

For biomolecules of increased size and flexibility, more efficient and reliable strategiesare always needed to determine their stable low-energy conformers. Here, we propose a fragment basedstep-by-step strategy to search for the full conformational space of biomolecules. In this strategy, themolecule is divided into several fragments and each of them is systematically optimized in a step-bystepfashion. It can significantly reduce the computational cost without losing any accuracy asdemonstrated by the conformer search of several representative di-/tri-/tetra- peptides. Such an approachwill be very useful for finding the stable conformers of large biomolecules.

Place, publisher, year, edition, pages
2014. Vol. 610, 303-309 p.
Keyword [en]
Fragment Based Step-by-Step Strategy
National Category
Natural Sciences
URN: urn:nbn:se:kth:diva-145198DOI: 10.1016/j.cplett.2014.07.054ISI: 000342527500056ScopusID: 2-s2.0-84905725347OAI: diva2:717159

Updated from submitted to published.


Available from: 2014-05-14 Created: 2014-05-14 Last updated: 2014-11-04Bibliographically approved
In thesis
1. Conformations of amino acids characterized by theoretical spectroscopy
Open this publication in new window or tab >>Conformations of amino acids characterized by theoretical spectroscopy
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Amino acids are the basic building blocks of proteins. The determinationof their structures plays an important role in correctly describing the functionsof the proteins. This thesis is devoted to theoretical studies on the potentialenergy surface of amino acids, in particular the infrared and soft X-ray spectralfingerprints of their most stable conformers.The stable structures of amino acids can be explored by different methods.We have used a full space systematic search strategy to determine the potentialenergy surface of deprotonated arginine and revealed several new conformers.With that, the calculated thermodynamic parameters are finally in good agreementwith their experimental counterparts. We have also proposed a molecularfragment based step-by-step strategy to search for the most stable conformers oflarge biomolecules. The high efficiency and good accuracy of this strategy havebeen firmly illustrated by the modeling of several polypeptides.Infrared (IR) spectroscopy has become one of the most applied techniques tocharacterize the structures of gas-phase amino acids. A direct comparison betweenexperimental and calculated infrared spectra provides an efficient way to describethe conformation exchanges of the amino acids. It is found that the conformersof an amino acid are not always necessary to reach the thermal equilibrium undercertain experimental conditions. The local minima could be responsible for theappearance of the measured spectra. This important point has been highlightedby the calculations of deprotonated tyrosine and cysteine, as well as the arginine.The near-edge X-ray absorption fine structure (NEXAFS) spectra and X-rayphotoelectron spectra (XPS) have also been simulated for neutral, deprotonatedand protonated arginine. The influences of intra-, and intermolecular hydrogenbonds on the electronic structure of the arginine have been carefully examined. Itis suggested that the XPS is capable of distinguishing the canonical and zwitterinicisomers of arginine, and works much better than any other tools available.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. xiv, 82 p.
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:11
amino acids, spectroscopy
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
urn:nbn:se:kth:diva-145208 (URN)978-91-7595-175-1 (ISBN)
Public defence
2014-06-09, FA32, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 14:30 (English)

QC 20140522

Available from: 2014-05-22 Created: 2014-05-14 Last updated: 2014-05-22Bibliographically approved

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