7 research outputs found
Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA
The dynamics of RNA within the β-relaxation
region of 10
ps to 1 ns is crucial to its biological function. Because of its simpler
chemical building blocks and the lack of the side methyl groups, faster
relaxational dynamics of RNA compared to proteins can be expected.
However, the situation is actually opposite. In this work, the relaxational
dynamics of tRNA is measured by quasielastic neutron scattering and
analyzed using the mode coupling theory, originally developed for
glass-forming liquids. Our results reveal that the dynamics of tRNA
follows a log-decay within the β-relaxation region, which is
an important trait demonstrated by the dynamics of proteins. The dynamics
of hydrated tRNA and lysozyme compared in the time domain further
demonstrate that the slower dynamics of tRNA relative to proteins
originates from the difference in the folded states of tRNA and proteins,
as well as the influence of their hydration water
Direct Determination of Hydroxymethyl Conformations of Plant Cell Wall Cellulose Using <sup>1</sup>H Polarization Transfer Solid-State NMR
In
contrast to the well-studied crystalline cellulose of microbial
and animal origins, cellulose in plant cell walls is disordered due
to its interactions with matrix polysaccharides. Plant cell wall (PCW)
is an undisputed source of sustainable global energy; therefore, it
is important to determine the molecular structure of PCW cellulose.
The most reactive component of cellulose is the exocyclic hydroxymethyl
group: when it adopts the <i>tg</i> conformation, it stabilizes
intrachain and interchain hydrogen bonding, while <i>gt</i> and <i>gg</i> conformations destabilize the hydrogen-bonding
network. So far, information about the hydroxymethyl conformation
in cellulose has been exclusively obtained from <sup>13</sup>C chemical
shifts of monosaccharides and oligosaccharides, which do not reflect
the environment of cellulose in plant cell walls. Here, we use solid-state
Nuclear Magnetic Resonance (ssNMR) spectroscopy to measure the hydroxymethyl
torsion angle of cellulose in two model plants, by detecting distance-dependent
polarization transfer between H4 and H6 protons in 2D <sup>13</sup>C–<sup>13</sup>C correlation spectra. We show that the interior
crystalline portion of cellulose microfibrils in <i>Brachypodium</i> and <i>Arabidopsis</i> cell walls exhibits H4–H6
polarization transfer curves that are indicative of a <i>tg</i> conformation, whereas surface cellulose chains exhibit slower H4–H6
polarization transfer that is best fit to the <i>gt</i> conformation.
Joint constraints by the H4–H6 polarization transfer curves
and <sup>13</sup>C chemical shifts indicate that it is unlikely for
interior cellulose to have a significant population of the <i>gt</i> and <i>gg</i> conformation mixed with the <i>tg</i> conformation, while surface cellulose may adopt a small
percentage of the <i>gg</i> conformation. These results
provide new constraints to the structure and matrix interactions of
cellulose in plant cell walls, and represent the first direct determination
of a torsion angle in an important noncrystalline carbohydrate polymer
<i>In Vivo</i> Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale
Selectively labeled
GroEL protein was produced in living deuterated
bacterial cells to enhance its neutron scattering signal above that
of the intracellular milieu. Quasi-elastic neutron scattering shows
that the in-cell diffusion coefficient of GroEL was (4.7 ± 0.3)
× 10<sup>–12</sup> m<sup>2</sup>/s, a factor of 4 slower
than its diffusion coefficient in buffer solution. Internal protein
dynamics showed a relaxation time of (65 ± 6) ps, a factor of
2 slower compared to the protein in solution. Comparison to the literature
suggests that the effective diffusivity of proteins depends on the
length and time scale being probed. Retardation of in-cell diffusion
compared to the buffer becomes more significant with the increasing
probe length scale, suggesting that intracellular diffusion of biomolecules
is nonuniform over the cellular volume. The approach outlined here
enables investigation of protein dynamics within living cells to open
up new lines of research using “in-cell neutron scattering”
to study the dynamics of complex biomolecular systems
Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity
In this article, we elucidate the
protein activity from the perspective
of protein softness and flexibility by studying the collective phonon-like
excitations in a globular protein, human serum albumin (HSA), and
taking advantage of the state-of-the-art inelastic X-ray scattering
(IXS) technique. Such excitations demonstrate that the protein becomes
softer upon thermal denaturation due to disruption of weak noncovalent
bonds. On the other hand, no significant change in the local excitations
is detected in ligand- (drugs) bound HSA compared to the ligand-free
HSA. Our results clearly suggest that the protein conformational flexibility
and rigidity are balanced by the native protein structure for biological
activity
Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study
Nontoxic, biocompatible nanodiamonds
(ND) have recently been implemented
in rational, systematic design of optimal therapeutic use in nanomedicines.
However, hydrophilicity of the ND surface strongly influences structure
and dynamics of biomolecules that restrict <i>in situ</i> applications of ND. Therefore, fundamental understanding of the
impact of hydrophilic ND surface on biomolecules at the molecular
level is essential. For tRNA, we observe an enhancement of dynamical
behavior in the presence of ND contrary to generally observed slow
motion at strongly interacting interfaces. We took advantage of neutron
scattering experiments and computer simulations to demonstrate this
atypical faster dynamics of tRNA on ND surface. The strong attractive
interactions between ND, tRNA, and water give rise to unlike dynamical
behavior and structural changes of tRNA in front of ND compared to
without ND. Our new findings may provide new design principles for
safer, improved drug delivery platforms
Description of Hydration Water in Protein (Green Fluorescent Protein) Solution
The structurally and dynamically
perturbed hydration shells that
surround proteins and biomolecules have a substantial influence upon
their function and stability. This makes the extent and degree of
water perturbation of practical interest for general biological study
and industrial formulation. We present an experimental description
of the dynamical perturbation of hydration water around green fluorescent
protein in solution. Less than two shells (∼5.5 Å) were
perturbed, with dynamics a factor of 2–10 times slower than
bulk water, depending on their distance from the protein surface and
the probe length of the measurement. This dependence on probe length
demonstrates that hydration water undergoes subdiffusive motions (τ
∝ <i>q</i><sup>–2.5</sup> for the first hydration
shell, τ ∝ <i>q</i><sup>–2.3</sup> for
perturbed water in the second shell), an important difference with
neat water, which demonstrates diffusive behavior (τ ∝ <i>q</i><sup>–2</sup>). These results help clarify the seemingly
conflicting range of values reported for hydration water retardation
as a logical consequence of the different length scales probed by
the analytical techniques used
Understanding Multiscale Structural Changes During Dilute Acid Pretreatment of Switchgrass and Poplar
Biofuels
produced from lignocellulosic biomass hold great promise
as a renewable alternative energy and fuel source. To realize a cost
and energy efficient approach, a fundamental understanding of the
deconstruction process is critically necessary to reduce biomass recalcitrance.
Herein, the structural and morphological changes over multiple scales
(5–6000 Å) in herbaceous (switchgrass) and woody (hybrid
poplar) biomass during dilute sulfuric acid pretreatment were explored
using neutron scattering and X-ray diffraction. Switchgrass undergoes
a larger increase (20–84 Å) in the average diameter of
the crystalline core of the elementary cellulose fibril than hybrid
poplar (19–50 Å). Switchgrass initially forms lignin aggregates
with an average size of 90 Å that coalesce to 200 Å, which
is double that observed for hybrid poplar, 55–130 Å. Switchgrass
shows a smooth-to-rough transition in the cell wall surface morphology
unlike the diffuse-to-smooth transition of hybrid poplar. Yet, switchgrass
and hybrid poplar pretreated under the same experimental conditions
result in pretreated switchgrass producing higher glucose yields (∼76
wt %) than pretreated hybrid poplar (∼60 wt %). This observation
shows that other aspects like cellulose allomorph transitions, cellulose
accessibility, cellular biopolymer spatial distribution, and enzyme–substrate
interactions may be more critical in governing the enzymatic hydrolysis
efficiency