Nature and magnitude of aromatic stacking of nucleic acid bases
J Šponer, KE Riley, P Hobza - Physical Chemistry Chemical Physics, 2008 - pubs.rsc.org
This review summarises recent advances in quantum chemical calculations of base-stacking
forces in nucleic acids. We explain in detail the very complex relationship between the gas …
forces in nucleic acids. We explain in detail the very complex relationship between the gas …
Numerical methods for electronic structure calculations of materials
The goal of this article is to give an overview of numerical problems encountered when
determining the electronic structure of materials and the rich variety of techniques used to …
determining the electronic structure of materials and the rich variety of techniques used to …
Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases
P Mignon, S Loverix, J Steyaert… - Nucleic Acids …, 2005 - academic.oup.com
The interplay between aromatic stacking and hydrogen bonding in nucleobases has been
investigated via high-level quantum chemical calculations. The experimentally observed …
investigated via high-level quantum chemical calculations. The experimentally observed …
How well can new-generation density functional methods describe stacking interactions in biological systems?
Y Zhao, DG Truhlar - Physical Chemistry Chemical Physics, 2005 - pubs.rsc.org
We compare the performance of four recently developed DFT methods (MPW1B95,
MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods …
MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods …
Nature of base stacking: reference quantum‐chemical stacking energies in ten unique B‐DNA base‐pair steps
J Šponer, P Jurečka, I Marchan… - … A European Journal, 2006 - Wiley Online Library
Base‐stacking energies in ten unique B‐DNA base‐pair steps and some other
arrangements were evaluated by the second‐order Møller–Plesset (MP2) method, complete …
arrangements were evaluated by the second‐order Møller–Plesset (MP2) method, complete …
Aromatic− aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues
S Aravinda, N Shamala, C Das… - Journal of the …, 2003 - ACS Publications
Aromatic− aromatic interactions between phenylalanine side chains in peptides have been
probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val …
probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val …
Design and NMR characterization of active analogues of compstatin containing non-natural amino acids
B Mallik, M Katragadda, LA Spruce… - Journal of Medicinal …, 2005 - ACS Publications
We present new findings in our drug discovery effort to develop an anticomplement
therapeutic. We have designed several active analogues of compstatin by altering its amino …
therapeutic. We have designed several active analogues of compstatin by altering its amino …
An intramembrane aromatic network determines pentameric assembly of Cys-loop receptors
S Haeger, D Kuzmin, S Detro-Dassen, N Lang… - Nature structural & …, 2010 - nature.com
Cys-loop receptors are pentameric ligand-gated ion channels (pLGICs) that mediate fast
synaptic transmission. Here functional pentameric assembly of truncated fragments …
synaptic transmission. Here functional pentameric assembly of truncated fragments …
Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in …
J Isaksson, S Acharya, J Barman, P Cheruku… - Biochemistry, 2004 - ACS Publications
The structural preorganization of isosequential ssDNA and ssRNA hexamers d/r (GAAAAC)
1 [J. Am. Chem. Soc. 2003, 125, 9948] have been investigated by NMR and molecular …
1 [J. Am. Chem. Soc. 2003, 125, 9948] have been investigated by NMR and molecular …
Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids
LR Rutledge, LS Campbell-Verduyn… - Chemical physics letters, 2007 - Elsevier
MP2/6-31G∗(0.25) gas-phase potential energy surfaces of stacked dimers between the four
aromatic amino acids and the natural (DNA or RNA) nucleobases were considered as a …
aromatic amino acids and the natural (DNA or RNA) nucleobases were considered as a …