Classical molecular dynamics (MD) simulations are useful for characterizing the structure and dynamics of biological macromolecules, ultimately, resulting in elucidation of biological function. The AMBER force field is widely used and has well-defined bond length, bond angle, partial charge, and van der Waals parameters for all the common amino acids and nucleotides, but it lacks parameters for many of the modifications found in nucleic acids and proteins. Presently there are 107 known naturally occurring modifications that play important roles in RNA stability, folding, and other functions. Modified nucleotides are found in almost all transfer RNAs, ribosomal RNAs of both the small and large subunits, and in many other functional RNAs. We developed force field parameters for the 107 modified nucleotides currently known to be present in RNA. The methodology used for deriving the modified nucleotide parameters is consistent with the methods used to develop the Cornell et al. force field. These parameters will improve the functionality of AMBER so that simulations can now be readily performed on diverse RNAs having post-transcriptional modifications.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/ct600329w | DOI Listing |
J Mol Graph Model
December 2024
CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India. Electronic address:
Multi-scale models in which varying resolutions are considered in a single molecular dynamics simulation setup are gaining importance in integrative modeling. However, combining atomistic and coarse-grain resolutions, especially for coarse-grain force fields derived from top-down approaches, have not been well explored. In this study, we have implemented and tested a dual-resolution simulation approach to model globular proteins in atomistic detail (represented by the CHARMM36 model) with the surrounding solvent in Martini2 coarse-grain detail.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, Palaiseau, France.
Folates comprise a crucial class of biologically active compounds related to folic acid, playing a vital role in numerous enzymatic reactions. One-carbon metabolism, facilitated by the folate cofactor, supports numerous physiological processes, including biosynthesis, amino acid homeostasis, epigenetic maintenance, and redox defense. Folates share a common pterin heterocyclic ring structure capable of undergoing redox reactions and existing in various protonation states.
View Article and Find Full Text PDFJ Anthropol Sci
December 2024
Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Italy,
Founded in 1894, the Museum "G. Sergi" houses a variety of osteological materials and other collections, including several plaster facial casts from different human populations. This paper investigates this collection, which has been acquired (at least in part) in the framework of Italian colonialism, focusing on expeditions respectively led by Lidio Cipriani and Corrado Gini during the fascist regime.
View Article and Find Full Text PDFJ Formos Med Assoc
December 2024
Division of Colorectal Surgery, Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, 100225, Taiwan. Electronic address:
Background: Surgical smoke generated by energy devices poses health risks to medical staff. During laparoscopic surgery, the smoke aggregating around the camera obstructs the visual field, forcing surgeons to interrupt surgery, and may increase surgical risk. We propose a proximal smoke evacuation method to improve surgical quality by effectively eliminating surgical smoke.
View Article and Find Full Text PDFHastings Cent Rep
December 2024
The promise of genomic medicine lies in the opportunity to improve health outcomes via a personalized approach to management, grounded in genetic and genomic variation unique to an individual. However, disparities and inequities mar this remarkable landscape of genomic innovation. Prior efforts to understand these inequities have focused on populations for which genetic testing is relatively protocolized or where test utility varies greatly by ancestry groups, where equitable outcomes are more clearly defined.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!