Criterion that determines the foldability of proteins.
نویسندگان
چکیده
We show, using lattice models of proteins, how the kinetic accessibility of the native state of proteins is encoded in the primary sequence itself. The folding times for various sequences correlate extremely well with the single parameter intrinsic to the sequence, namely, s jTu 2 Tf jyTu where Tu and Tf are the collapse and folding transition temperatures. Fast folding sequences have small values of s (typically less than 0.1) whereas s values for slow folding sequences exceed 0.6. The folding times change by 5 orders of magnitude when s goes from 0.05 to a value exceeding about 0.6. [S0031-9007(96)00175-5]
منابع مشابه
Comment on"A Criterion that determines foldability of proteins"by D. Klimov and D. Thirumalai (PRL,v.76, p.4070 (1996))
Comment on " A Criterion that determines foldability of proteins " by D.Klimov and D.Thirumalai The paper by Klimov and Thirumalai (KT) [1] presents results for protein folding obtained from Monte Carlo lattice model simulations of the type introduced in [2]. They draw two conclusions from their study of 15-mers and 27-mers. The first conclusion is that there exists a strong correlation between...
متن کاملReply to Comment on"Criterion that Determines the Foldability of Proteins"
We point out that the correlation between folding times and σ = (T θ − T f)/T θ in protein-like heteropolymer models where T θ and T f are the collapse and folding transition temperatures was already established in 1993 before the other presumed equivalent criterion (folding times correlating with T f alone) was suggested. We argue that the folding times for these models show no useful correlat...
متن کاملEffect of alphabet size and foldability requirements on protein structure designability.
A number of investigators have addressed the issue of why certain protein structures are especially common by considering structure designability, defined as the number of sequences that would successfully fold into any particular native structure. One such approach, based on foldability, suggested that structures could be classified according to their maximum possible foldability and that this...
متن کاملUniversal correlation between energy gap and foldability for the random energy model and lattice proteins
The random energy model, originally used to analyze the physics of spin glasses, has been employed to explore what makes a protein a good folder versus a bad folder. In earlier work, the ratio of the folding temperature over the glass–transition temperature was related to a statistical measure of protein energy landscapes denoted as the foldability F. It was posited and subsequently established...
متن کاملComparative Study of Hydrophobic-Polar and Miyazawa-Jernigan Energy Functions in Protein Folding on a Cubic Lattice Using Pruned-Enriched Rosenbluth Monte Carlo Algorithm
In this analysis of the contact energies guiding the protein folding, the performance of the PERM algorithm on a simple, cubic lattice is examined when Miyazawa-Jernigan (MJ) and Hydrophobic-Polar (HP) energy matrices are applied. Geometric similarity of minimum energy conformations of twenty proteins, generated when HP and MJ are used, is determined by the Root Mean Square Difference (RMSD) an...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Physical review letters
دوره 76 21 شماره
صفحات -
تاریخ انتشار 1996