Collective dynamics of the ribosomal tunnel revealed by elastic network modelingProteins: Structure, Function and Bioinformatics - Tập 75 Số 4 - Trang 837-845 - 2009
Özge Kürkçüoğlu, Zeynep Kurkcuoglu, Pemra Doruker, Robert L. Jernigan
AbstractThe collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motion...... hiện toàn bộ
What are the dielectric “constants” of proteins and how to validate electrostatic models?Proteins: Structure, Function and Bioinformatics - Tập 44 Số 4 - Trang 400-417 - 2001
Claudia Schütz, A. Warshel
AbstractImplicit models for evaluation of electrostatic energies in proteins include dielectric constants that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielectric constant. Furthermore, the factors that determine the optimal value of these constants are far from bein...... hiện toàn bộ
Crystallization and preliminary X‐ray diffraction studies of human salivary α‐amylaseProteins: Structure, Function and Bioinformatics - Tập 11 Số 3 - Trang 230-232 - 1991
N. Ramasubbu, K. K. Bhandary, Frank A. Scannapieco, M.J. Levine
AbstractNonglycosylated α‐amylase, a major component of human parotid saliva, has been crystallized by the vapor diffusion technique using 2‐methyl‐2,4‐pentanediol as the precipitant in the presence of CaCl2 at pH 9.0. The crystals are orthorhombic, space group P21212... hiện toàn bộ
Long timestep dynamics of peptides by the dynamics driver approachProteins: Structure, Function and Bioinformatics - Tập 21 Số 4 - Trang 282-302 - 1995
Philippe Derreumaux, Tamar Schlick
AbstractPrevious experience with the Langevin/implicit‐Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5–20 fs range but quenches high‐frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13‐residue oligoalanine...... hiện toàn bộ
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case studyProteins: Structure, Function and Bioinformatics - Tập 21 Số 3 - Trang 196-213 - 1995
Philippe H. Hünenberger, Alan E. Mark, Wilfred F. van Gunsteren
AbstractFour methods are compared to drive the unfolding of a protein: (1) high temperature (T‐run), (2) high pressure (P‐run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F‐run, radial force driven unfolding), and (4) by weak coupling of the difference between the tempera...... hiện toàn bộ
Comparing short protein substructures by a method based on backbone torsion anglesProteins: Structure, Function and Bioinformatics - Tập 6 Số 2 - Trang 155-167 - 1989
Mary E. Karpen, Pieter L. De Haseth, Kenneth Neet
AbstractAn efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes Δt, the root mean square difference in ϕ and ψ torsion angles over a small number of amino acids (typically 3–5). Using this algorithm, large number of protein substrates co...... hiện toàn bộ