اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدSpectroscopy, Dynamics and Hydration of S-Nitrosylated Myoglobin
73
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation in the condensed phase is investigated for the methyl-capped cysteine model system and for myoglobin. Using conventional point charge and physically more realistic multipolar force fields for the -SNO group it is found that the SN- and NO-stretch and the SNO-bend vibrations can be located and distinguished from the other protein modes for simulations of MbSNO at 50 K. The finding of stable cis- and trans-MbSNO is consistent with experiments on other proteins as is the observation of buried -SNO. For MbSNO the observed relocation of the EF loop in the simulations by $sim 3$ AA/ is consistent with the available X-ray structure and the conformations adopted by the -SNO label are in good overall agreement with the X-ray structure. Despite the larger size of the -SNO group, MbSNO is found to recruit more water molecules within 10 AA/ of the modification site than WT Mb due to the stronger electrostatics. Similarly, when comparing the hydration between the A- and H-helices they differ by up to 30 % between WT and MbSNO. This suggests that local hydration can also be significantly modulated through nitrosylation.
قيم البحث
اقرأ أيضاً
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes, chemistries, and
biological functions, and characterize their interactions with their hydration waters using molecular simulation and enhanced sampling techniques. We find that akin to extended hydrophobic surfaces, proteins situate their hydration waters at the edge of a dewetting transition, making them susceptible to unfavorable perturbations. We also find that the strength of the unfavorable potential needed to trigger dewetting is roughly the same, regardless of the protein being studied, and depends only the width of the hydration shell being perturbed. Our findings establish a framework for systematically classifying protein patches according to how favorably they interact with water.
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which
are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.
Combining two-color infared pump-probe spectroscopy and anharmonic force field calculations we characterize the anharmonic coupling patterns between fingerprint modes and the hydrogen-bonded symmetric NH$_2$ stretching vibration in adenine-thymine dA
$_{20}$-dT$_{20}$ DNA oligomers. Specifically, it is shown that the anharmonic coupling between the NH$_2$ bending and the CO stretching vibration, both absorbing around 1665 cm-1, can be used to assign the NH$_2$ fundamental transition at 3215 cm-1 despite the broad background absorption of water.
The electronic excitation population and coherence dynamics in the chromophores of the photosynthetic light harvesting complex 2 (LH2) B850 ring from purple bacteria (Rhodopseudomonas acidophila) have been studied theoretically at both physiological
and cryogenic temperatures. Similar to the well-studied Fenna-Matthews-Olson (FMO) protein, oscillations of the excitation population and coherence in the site basis are observed in LH2 by using a scaled hierarchical equation of motion (HEOM) approach. However, this oscillation time (300 fs) is much shorter compared to the FMO protein (650 fs) at cryogenic temperature. Both environment and high temperature are found to enhance the propagation speed of the exciton wave packet yet they shorten the coherence time and suppress the oscillation amplitude of coherence and the population. Our calculations show that a long-lived coherence between chromophore electronic excited states can exist in such a noisy biological environment.
Path-integral ab initio molecular dynamics (PI-AIMD) calculations have been employed to probe the nature of chloride ion solvation in aqueous solution. Nuclear quantum effects (NQEs) are shown to weaken hydrogen bonding between the chloride anion and
the solvation shell of water molecules. As a consequence, the disruptive effect of the anion on the solvent water structure is significantly reduced compared to what is found in the absence of NQEs. The chloride hydration structure obtained from PI-AIMD agrees well with information extracted from neutron scattering data. Inparticular, the observed satellite peak in the hydrogen-chloride-hydrogen triple angular distribution serves as a clear signature of NQEs. The present results suggest that NQEs are likely to play acrucial role in determining the structure of saline solutions.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
