New energy terms for reduced protein models implemented in an off‐lattice force field
- T. Hassinen, M. Peräkylä
- ChemistryJournal of Computational Chemistry
- 1 September 2001
Parameterization and test calculations of a reduced protein model with new energy terms are presented. The new energy terms retain the steric properties and the most significant degrees of freedom of…
4D prediction of protein 1H chemical shifts
- Juuso Lehtivarjo, T. Hassinen, Samuli-Petrus Korhonen, M. Peräkylä, R. Laatikainen
- ChemistryJournal of Biomolecular NMR
- 30 October 2009
A 4D approach for protein 1H chemical shift prediction was explored, and X-ray structures gave better predictions than the corresponding NMR structures, indicating that chemical shifts contain invaluable information about local structures.
Birch PR-10c interacts with several biologically important ligands.
- K. Koistinen, P. Soininen, S. Kärenlampi
- Biology, ChemistryPhytochemistry
- 1 November 2005
Antagonist- and inverse agonist-driven interactions of the vitamin D receptor and the constitutive androstane receptor with corepressor protein.
- Harri Lempiäinen, Ferdinand Molnár, M. Macias González, M. Peräkylä, C. Carlberg
- Biology, ChemistryMolecular Endocrinology
- 1 September 2005
The comparable molecular mechanisms that explain the similar functional profile of antagonist and inverse agonists are likely to be extended from VDR and CAR to other members of the NR superfamily and may lead to the design of even more effective ligands.
Amino Acids Important for Ligand Specificity of the Human Constitutive Androstane Receptor*
- Johanna Jyrkkärinne, B. Windshügel, P. Honkakoski
- Biology, ChemistryJournal of Biological Chemistry
- 18 February 2005
These studies identified several amino acids within helices 3 (Ile164 and Asn165), 5 (Val199), 11 (Tyr326, Ile330, and Gln331), and 12 (Leu343 and Ile346) that contribute to the high basal activity of human CAR.
Muscarinic Toxin 7 Selectivity Is Dictated by Extracellular Receptor Loops*
- Anu M. Kukkonen, M. Peräkylä, K. Åkerman, J. Näsman
- Biology, ChemistryJournal of Biological Chemistry
- 3 December 2004
The results indicate that the high selectivity of MT7 for the M1 receptor depends on very few residues, thus providing good prospects for future design and synthesis of muscarinic receptor-selective ligands.
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
- Juuso Lehtivarjo, K. Tuppurainen, T. Hassinen, R. Laatikainen, M. Peräkylä
- Chemistry, BiologyJournal of Biomolecular NMR
- 8 February 2012
The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction.
A structural basis for the species-specific antagonism of 26,23-lactones on vitamin D signaling.
- M. Peräkylä, Ferdinand Molnár, C. Carlberg
- Biology, ChemistryChemistry and Biology
- 1 August 2004
Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations
- M. Peräkylä
- Biology, ChemistryEuropean Biophysics Journal
- 1 February 2009
The pathways observed in a large number of relatively short random acceleration molecular dynamics trajectories were found to be in fair agreement, both in terms of pathway locations and deduced relative preferences, compared to targeted molecular dynamics (TMD) and streered molecular dynamics simulations (SMD).
Why Does Trypsin Cleave BPTI so Slowly
- M. Peräkylä, P. Kollman
- Biology, Chemistry
- 24 March 2000
Evidence is provided to support the hypothesis that the remaining 102−105 decrease in rate arises from the fact that the peptide bond in BPTI, once cleaved, is much more likely to re-ligate than to be further hydrolyzed to form products which will be released from trypsin.
...
...