摘要:

AbstractTwo cyclic hexapeptides, cyclo[Ala1‐D‐Ala2‐Ser3‐Phe4‐Gly5‐Ser6] and cyclo[Ala1‐Gly2‐Ser3‐Phe4‐Gly5‐Ser6], derived from the loop portion of the C′C″ ridge of CD4, were characterized by high‐resolution nmr spectroscopy and simulated annealing studies. In DMSO‐d6both of these peptides display a single conformer on the nmr time scale with two intramolecular H‐bond (1 ← 4) stabilized β‐turns at positions 2–3 and 5–6. The nmr derived distance constraints were used in simulated annealing calculations to generate the solution structures. These structures adopt energetically comparable conformational substates that are not resolvable on the nmr time scale. In aqueous solution, the H‐bond stabilized β‐turn conformation for cyclo [Ala‐D‐Ala‐Ser‐Phe‐Gly‐Ser] is no longer the predominant structural form. Structures generated using molecular dynamics simulations with no experimental constraints were compared with those from nmr analysis. The correlation between these two sets of structures allows the use of molecular simulations as a predictive tool for the conformationa

ISSN:0006-3525    

DOI:10.1002/bip.360340802

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractCooperative phenomena in biological macromolecules arise from the interaction of many distinct subsystems, such as structural domains or binding sites. Cooperative properties of the system as a whole, like protein folding or allosteric transitions, are subject to the restrictions imposed by thermodynamic stability. These restrictions, however, do not apply in the case of individual subsystems open to interactions with the rest of the macromolecule. The site‐specific properties of such subsystems can be understood in general thermodynamic terms from those of a multicomponent system under particular conditions. The analogy provides a thermodynamic basis for site‐specific Cooperativity. © 1994 John Wiley&Sons,

ISSN:0006-3525    

DOI:10.1002/bip.360340803

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractThe crystal structure of cyclo(Pro‐Gly)3(PG3) complex with LiSCN (C22H30N7O6SLi) has been solved by x‐ray diffraction. The crystals belong to the space group R3 in the hexagonal setting with unit cell parameters ofa= 12.581(1),c= 29.705(3) Å,V= 4072.0 Å3,Z= 6,Mr= 527.53,Dc= 1.23 g/cm3. The crystal structure was solved by direct methods using the program SHELXS‐86 and refined to anRvalue of 5.3% for 1645 reflections (I>2σI). There are two conformers in the crystal structure. One conformer has three carbonyls on one side and three on the other side of the peptide plane. The other conformer has all six of the carbonyls on the same side of the peptide plane. Both of these conformers bind independently to a Li ion. Based on the conformers of the Li complex and other reported ion complexes formed by PG3, we propose a model for the transport of ions across the lipid membrane. The features of the model are as follows: (1) PG3 forms a hexameric stack in a lipid bilayer when complexing and transporting metal ions. (2) It undergoes a conformational flipping in order pass the ion along the channel. The energy required for the conformational change involved in the flipping of the PG3 molecule may be provided by the applied potential during ion transport. © 1994 John Wiley&

ISSN:0006-3525    

DOI:10.1002/bip.360340804

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractA model for solvation in mixed solvents, which was developed for the free energy and preferential interaction [J. A. Schellman (1987),Biopolymers, Vol. 26, pp. 549–559; (1990),Biophysical Chemistry, Vol. 37, pp. 121–140; (1993),Biophysical Chemistry, Vol. 45, pp. 273–279], is extended in this paper to cover the thermal properties: enthalpy, entropy, and heat capacity. An important result is that the enthalpy of solvationH̄ 2exresponds directly to the fraction of site occupation. This differs from the free energyḠ 2exand preferential interaction Γ32, which are measures of the excess binding above a random distribution of solvent molecules. In other words, the enthalpy is governed byKwhileḠ 2exand Γ32are governed by (K− 1) whereKis the equilibrium constant on a mole fraction scale [Schellman (1987)].The solvation heat capacityC̄p 2exconsists of two term: (1) the intrinsic heat capacity of species in solution with no change in composition, and (2) a term that accounts for the change in composition that accompanies solvent exchange.Binding to biological macromolecules is heterogeneous but experiementalists must use binding isotherms that assume the homogeneity of sites. Equations are developed for the interpretation of the experimental parameters (number of sitesnexp, equilibrium constantKexp, and enthalpy, Δhexp), when homogeneous formulas are applied to the heterogeneous case. It is shown that the experimental parameters for the occupation and enthalpy are simple functions of the moments of the distribution of equilibrium constants over the sites. In general,nexpis greater than the true number of sites andKexpis greater than the average of the equilibrium constants. The free energy and preferential interaction can be fit to a homogenious formula, but the parameters of the curve are not easily represented in terms of the moments of distributions over the sites.The strengths and deficiencies of this type of thermodynamic model are discussed. ©

ISSN:0006-3525    

DOI:10.1002/bip.360340805

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractWe have used the molecular dynamics (MD) simulation package AMBER4 to search the conformation of a peptide predicted as a leucine zipper motif for the human immunodeficiency virus type I integrase protein (HIV IN‐LZM). The peptide is composed of 22 amino acid residues and its location is from Val 151 to Leu 172. The searching procedure also includes two known α‐helices that served as positive controls—namely, a 22‐residue GCN4‐p1 (LZM) and a 20‐residue poly(L‐alanine) (PLA). A 21‐residue peptide extracted from a cytochrome C crystal (CCC‐t) with determined conformation as a β‐turn is also included as a negative control. At the beginning of the search, two starting conformations—namely, the standard right‐handed α‐helix and the fully stretched conformations—are generated for each peptide. Structures generated as standard α‐helix are equilibrated at room temperature for 90 ps while structures generated as a fully stretched one are equilibrated at 600 K for 120 ps. The CCC‐t and PLA helices are nearly destroyed from the beginning of equilibration. However, for both the HIV IN‐LZM and the GCN4‐p1 LZM structures, there is substantial helicity being retained throughout the entire course of equilibration. Although helix propagation profiles calculated indicate that both peptides possess about the same propensity to form an α‐helix, the HIV IN‐LZM helix appears to be more stable than the GCN4‐p1 one as judged by a variety of analyses on both structures generated during the equilibration course. The fact that predicted HIV IN‐LZM can exist as an α‐helix is also supported by the results of high temperature equilibration run on the fully stretched structures generated. In this run, the RMS deviations between the backbone atoms of the structures with the lowest potential energy (PE) identified within every 2 ps and the structure with the lowest PE searched in the same course of simulation are calculated. For both the HIV IN‐LZM and the GCN4‐p1 LZM, these rms values decrease with the decrease of PE, which indicates that both structures are closer in conformations as their PEs are mov

ISSN:0006-3525    

DOI:10.1002/bip.360340806

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractIn order to investigate the conformational preferences to elicit tastes, conformational free energy calculations using an empirical potential (ECEPP/2) and the hydration shell model were carried out on theL‐aspartyl dipeptide methyl esters,L‐+HAsp−‐L‐Xaa‐OMe, in the hydrated state, where Xaa includes sweet (Phe, Tyr, Met, and Gly), bitter (Ala, Trp, Val, Leu, and Ile), and tasteless (Ser, Thr, and Abu) residues. The refined preferred conformation of the Phe dipeptide (aspartame) with side chain χ 21conformationg−isg−Fg−in the hydrated state, which is consistent with the structure deduced from1H‐nmr experiments. Irrespective of the Xaa and taste, all the dipeptides have the same conformation for the Asp residue, which is attributable to the hydrogen bond between protonated amino hydrogen and carboxylate oxygen and the favored hydration of the carboxylate group. This implies that theL‐aspartyl residue is a necessary factor for the dipeptides to be sweet not a sufficient factor. The computed conformational preferences for sweet, bitter, and tasteless dipeptides in the hydrated state indicate to us that the conformation about the NCαbond of the Xaa residue, i.e., the orientation of the hydrophobic moiety with respect to the AH/B functionalities in the aspartyl moiety, seems to be crucial to elicit the tastes. In addition, the hydrophobicity and the size of the Xaa residue are found to play a major role in determining the tastes. These well accord with the related works reported previously.

ISSN:0006-3525    

DOI:10.1002/bip.360340807

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractThe morphology and primary crystal structure of SLPF, a protein polymer produced by genetically engineeredEscherichia colibacteria, were characterized. SLPF is a segmented copolymer consisting of amino acid sequence blocks modeled on the crystalline segments of silk fibroin and the cell attachment domain of human fibronectin. Wide angle x‐ray scattering (WAXS), transmission electron microscopy (TEM), selected area electron diffraction (SAED), and molecular simulations were used to analyze the primary crystal structure of SLPF. TEM experiments conducted on SLPF droplets cast from formic acid on amorphous carbon film demonstrated that these protein films have a microstructure formed of woven sheaves. The sheaves are composed of well‐defined whisker crystallites. The width of the whiskers, 11.8 ± 2.2 nm, may be correlated to the length of the silk‐like segment in SLPF as predicted by molecular simulations. WAXS data, TEM images, SAED, patterns, molecular simulations, and theoretical diffraction patterns all were consistent with the crankshaft model proposed for Silk I by Lotz and Keith. © 1994 John Wiley&So

ISSN:0006-3525    

DOI:10.1002/bip.360340808

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractThe comparative interaction of Mg2+and Ca2+counterions on carboxyl groups of polygalacturonic acid is developed. Ultracentrifugation, conductimetry, potentiometry, and CD were used in this work. Evidence is provided for a simple electrostatic interaction of Mg2+counterions; on the opposite side, cooperative interaction of Ca2+counterions is again demonstrated, causing chain–chain association. © 1994 John Wiley&Sons, I

ISSN:0006-3525    

DOI:10.1002/bip.360340809

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractThe ir and Raman spectra ofL‐aspartic acid,L‐aspartic‐d4acid, andL‐aspartic‐15N acid as solid samples have been recorded and measured. The data obtained were used to propose a general assignment of the fundamental vibrational modes in the basis of the isotopic shifts measured and correlations with previous data reported for other amino acids and related molecules. A MNDO‐scaled semiempirical force field was obtained, and vibrational frequencies and descriptions were used to support the previous assignments based on experimental features. © 1994 John Wil

ISSN:0006-3525    

DOI:10.1002/bip.360340810

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY

摘要:

AbstractMolecular dynamics simulations in vacuum and solution have been carried out on 2′‐α‐L‐fucosyllactitol, a model for blood group H in conjunction with two‐dimensional nmr measurements on the same compound. Three independent starting conformations for the dynamics were chosen from low energy conformations obtained by a ϕ/ψ grid search. Nine 5 ns vacuum simulations of the trisaccharide were performed, employing three different ways to treat electrostatic interactions for each starting conformation: distance‐dependent dielectric with ε =r, constant dielectric with ε = 1, or constant dielectric with ε = 80. In vacuum, transitions of ϕ and ψ for the α‐L‐Fuc‐(1 → 2)‐β‐D‐Gal element occur in a cooperative manner. The virtual distance obtained for H1 in fucose to H2 in galactose from nuclear Overhauser effect spectroscopy experiments agree with one of the conformations of the trisaccharide in one of the three 100 ps aqueous simulations (ϕ/ψ ca. −100°/150°), indicating this may be a dominant solution conformation. The rms fluctuations of the ϕ‐ and ψ‐dihedral angles were ∼ 10° for a conformational state, both in the vacuum and the aqueous simulations. For the simulations in vacuum, the agreement with experimental NOE data is reasonable when a constant dielectric of 1 is used (major conformers having ϕ/ψ ca. −100°/150° and −140°/100°), whereas the agreement was poor with a constant dielectric of 80. Translational diffusion coefficients calculated from the simulation of the oligosaccharides were 0.12–0.18 × 10−5cm2/s and fr

ISSN:0006-3525    

DOI:10.1002/bip.360340811

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1994

数据来源: WILEY