RNA Base Pair Folding Kinetics from MD Simulations: Force Field Dependence

نویسندگان
چکیده

برای دانلود باید عضویت طلایی داشته باشید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Force field bias in protein folding simulations.

Long timescale (>1 micros) molecular dynamics simulations of protein folding offer a powerful tool for understanding the atomic-scale interactions that determine a protein's folding pathway and stabilize its native state. Unfortunately, when the simulated protein fails to fold, it is often unclear whether the failure is due to a deficiency in the underlying force fields or simply a lack of suff...

متن کامل

Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality.

Comparing experimental generalized N-H S(2) order parameters to those calculated from molecular dynamics trajectories is increasingly used to judge force-field quality and completeness of sampling. Herein we demonstrate for the well-investigated system hen egg white lysozyme that different experimental starting structures can lead to significant differences in molecular-dynamics-derived S(2) pa...

متن کامل

RNA hairpin-folding kinetics.

Based on the complete ensemble of hairpin conformations, a statistical mechanical model that combines the eigenvalue solutions of the rate matrix and the free-energy landscapes has been able to predict the temperature-dependent folding rate, kinetic intermediates, and folding pathways for hairpin-forming RNA sequences. At temperatures higher than a "glass transition" temperature, T(g), the eige...

متن کامل

Dependence of A-RNA simulations on the choice of the force field and salt strength.

We present an extensive molecular dynamics study (0.6 micros in total) on three A-RNA duplexes. The dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions (approximately 0.18 M net-neutralizing Na(+) and approximately 0.3 M KCl) was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing te...

متن کامل

Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods.

Mechanical unfolding and refolding of single RNA molecules have previously been observed in optical traps as sudden changes in molecular extension. Two methods have been traditionally used: "force-ramp", with the applied force continuously changing, and "hopping". In hopping experiments the force is held constant and the molecule jumps spontaneously between two different states. Unfolding/refol...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

ژورنال

عنوان ژورنال: Biophysical Journal

سال: 2019

ISSN: 0006-3495

DOI: 10.1016/j.bpj.2018.11.1920