Analyzing the biopolymer folding rates and pathways using kinetic cluster method.

نویسندگان

  • Wenbing Zhang
  • Shi-Jie Chen
چکیده

A kinetic cluster method enables us to analyze biopolymer folding kinetics with discrete rate-limiting steps by classifying biopolymer conformations into pre-equilibrated clusters. The overall folding kinetics is determined by the intercluster transitions. Due to the complex energy landscapes of biopolymers, the intercluster transitions have multiple pathways and can have kinetic intermediates (local free-energy minima) distributed on the intercluster pathways. We focus on the RNA secondary structure folding kinetics. The dominant folding pathways and the kinetic partitioning mechanism can be identified and quantified from the rate constants for different intercluster pathways. Moreover, the temperature dependence of the folding rate can be analyzed from the interplay between the stabilities of the on-pathway (nativelike) and off-pathway (misfolded) conformations and from the kinetic partitioning between different intercluster pathways. The predicted folding kinetics can be directly tested against experiments.

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Kinetic Study and Equilibrium Isotherm Analysis of Nickel (II) Adsorption onto Alginate-SBA-15 Nanocomposite

The present work was undertaken to evaluate the feasibility of nickel (II) removal from aqueous solution by adsorption onto a biopolymer adsorbent. The adsorbent was prepared using modification of mesoporous silicate SBA-15 with alginate biopolymer (alginateSBA-15) by encapsulation method. Morphological structure of the obtained nanocomposite adsorbent was characterized by XRD, scanning electro...

متن کامل

A new computational approach for mechanical folding kinetics of RNA hairpins.

Based on an ensemble of kinetically accessible conformations, we propose a new analytical model for RNA folding kinetics. The model gives populational kinetics, kinetic rates, transition states, and pathways from the rate matrix. Applications of the new kinetic model to mechanical folding of RNA hairpins such as trans-activation-responsive RNA reveal distinct kinetic behaviors in different forc...

متن کامل

Master equation approach to finding the rate-limiting steps in biopolymer folding.

A master equation approach is developed to find the rate-limiting steps in biopolymer folding, where the folding kinetics is described as a linear combination of basic kinetic modes determined from the eigenvalues and eigenvectors of the rate matrix. Because the passage of a rate-limiting step is intrinsically related to the folding speed, it is possible to probe and to identify the rate-limiti...

متن کامل

Direct observation of kinetic traps associated with structural transformations leading to multiple pathways of S-layer assembly.

The concept of a folding funnel with kinetic traps describes folding of individual proteins. Using in situ Atomic Force Microscopy to investigate S-layer assembly on mica, we show this concept is equally valid during self-assembly of proteins into extended matrices. We find the S-layer-on-mica system possesses a kinetic trap associated with conformational differences between a long-lived transi...

متن کامل

Equilibrium kinetic network of the villin headpiece in implicit solvent.

We applied the single-replica multiple-state transition-interface sampling method to elucidate the equilibrium kinetic network of the 35-residue-fragment (HP-35) villin headpiece in implicit water at room temperature. Starting from the native Protein Data Bank structure, nine (meta)stable states of the system were identified, from which the kinetic network was built by sampling pathways between...

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

عنوان ژورنال:
  • The Journal of chemical physics

دوره 119 16  شماره 

صفحات  -

تاریخ انتشار 2003