Molecular dynamics simulations of small peptides: dependence on dielectric model and pH

V Daggett, PA Kollman, ID Kuntz - … : Original Research on …, 1991 - Wiley Online Library
There has been much interest recently in the structure of small peptides in solution. A recent
study by Bradley and co‐workers [(1989) in Techniques of Protein Chemistry, Hugli, TE, Ed …

Model simulations of DNA dynamics

F Zhang, MA Collins - Physical Review E, 1995 - APS
A simple physical model is developed to study some characteristics of DNA dynamics. The
model uses only a few degrees of freedom so that DNA dynamics can be simulated over …

Distance‐dependent dielectric constants and their application to double‐helical DNA

J Mazur, RL Jernigan - Biopolymers: Original Research on …, 1991 - Wiley Online Library
Detailed studies of structures of biological macromolecules, even in simplified models,
involve many costly and time‐consuming calculations. Any thorough methods require …

Toxicity and repair of DNA adducts produced by the natural product yatakemycin

EA Mullins, R Shi, BF Eichman - Nature chemical biology, 2017 - nature.com
Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial
and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin …

Role of base flipping in specific recognition of damaged DNA by repair enzymes

M Fuxreiter, N Luo, P Jedlovszky, I Simon… - Journal of molecular …, 2002 - Elsevier
DNA repair enzymes induce base flipping in the process of damage recognition.
Endonuclease V initiates the repair of cis, syn thymine dimers (TD) produced in DNA by UV …

Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches

PR Desai, S Brahmachari, JF Marko, S Das… - Nucleic acids …, 2020 - academic.oup.com
Damaged or mismatched DNA bases result in the formation of physical defects in double-
stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain …

Anatomy of highly expressing chromosomal sites targeted by retroviral vectors

C Mielke, K Maass, M Tümmler, J Bode - Biochemistry, 1996 - ACS Publications
The eukaryotic genome contains chromosomal loci with a high transcription-promoting
potential. For their identification in cultured cells, transfer of a reporter gene has to be …

The Trapping of a Spontaneously “Flipped-Out” Base from Double Helical Nucleic Acids by Host− Guest Complexation with β-Cyclodextrin: The Intrinsic Base-Flipping …

MA Spies, RL Schowen - Journal of the American Chemical …, 2002 - ACS Publications
β-Cyclodextrin, which forms stable host− guest complexes with purine bases, induces the
melting of RNA and DNA duplexes below their normal melting temperatures. α-Cyclodextrin …

DNA flexibility variation may dominate DNase I cleavage.

ME Hogan, MW Roberson… - Proceedings of the …, 1989 - National Acad Sciences
In a previous experimental study, we proposed that the bending and torsional stiffness of
DNA display a systematic sequence dependence. Subsequently, we developed an elastic …

Distance and exposure dependent effective dielectric function

B Mallik, A Masunov, T Lazaridis - Journal of Computational …, 2002 - Wiley Online Library
In an effort to develop a dielectric screening function for molecular dynamics simulations of
biomolecules in implicit solvent, effective dielectric constants (Deff) for a large number of …