Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA:
  Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical
  Simulations   Ions interacting with hydrated RNA play a central role in defining its
secondary and tertiary structure. While spatial arrangements of ions, water
molecules, and phosphate groups have been inferred from X-ray studies, the role
of electrostatic and other noncovalent interactions in stabilizing compact
folded RNA structures is not fully understood at the molecular level. Here, we
demonstrate that contact ion pairs of magnesium (Mg2+) and phosphate groups
embedded in local water shells stabilize the tertiary equilibrium structure of
transfer RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA from
Escherichia coli, we follow the population of Mg2+ sites close to phosphate
groups of the ribose-phosphodiester backbone step by step, combining linear and
nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics
simulations and ab initio vibrational frequency calculations. The formation of
up to six Mg2+/phosphate contact pairs per tRNA and local field-induced
reorientations of water molecules balance the phosphate-phosphate repulsion in
nonhelical parts of tRNA, thus stabilizing the folded structure
electrostatically. Such geometries display limited sub-picosecond fluctuations
in the arrangement of water molecules and ion residence times longer than 1
{\mu}s. At higher Mg2+ excess, the number of contact ion pairs per tRNA
saturates around 6 and weakly interacting ions prevail. Our results suggest a
predominance of contact ion pairs over long-range coupling of the ion
atmosphere and the biomolecule in defining and stabilizing the tertiary
structure of tRNA.

25
The categories of this paper are: patt-sol
28
The categories of this paper are: alg-geom
35
The categories of this paper are: mtrl-th
30
The categories of this paper are: q-alg
33
The categories of this paper are: plasm-ph
6
The categories of this paper are: astro-ph
32
The categories of this paper are: atom-ph
14
The categories of this paper are: math-ph
23
The categories of this paper are: solv-int
21
The categories of this paper are: adap-org
29
The categories of this paper are: funct-an
22
The categories of this paper are: chao-dyn
5
The categories of this paper are: gr-qc
18
The categories of this paper are: econ
31
The categories of this paper are: ao-sci
10
The categories of this paper are: q-bio