Protein type effects on steady-state crossflow membrane ultrafiltration fluxes and protein transmission

The permeate fluxes and percent protein transmission were evaluated for steady-state crossflow ultrafiltration of two proteins of different composition: bovine serum albumin (BSA), containing fatty acid, and “fatty-acid-poor” BSA, from which most of the fatty acids had been removed (BSA/FAP). The influences of protein concentration up to 6.5 percent w/v, transmembrane pressure, ionic environment and membrane type (i.e. nominal molecular weight cut-off) were investigated. For both BSA and BSA/FAP, the fluxes and the protein transmission were dependent on the amount of salt present. The higher fatty acid content in the BSA apparently enhanced protein-protein interaction, resulting in a more cohesive and resistant fouling layer; permeate fluxes were lower with BSA/FAP than with BSA at otherwise corresponding operating conditions. A hysteresis behaviour of the flux (J)-transmembrane pressure (TMP) relationship was observed whenever the ultrafiltration unit was operated at a TMP less than some higher value to which the membrane previously had been exposed.     

An electron microscopic study of the archaeal feast/famine regulatory protein 5. Fourier filtration of images

Microcrystals of the feast/famine regulatory protein (FFRP) pot0434017 (FL11) were prepared by sonicating larger crystals. Using the microcrystals a cryo-electron micrograph was obtained, which showed a hexagonal packing of cylinder-like assemblies of FL11. This micrograph was processed by selecting, in the Fourier space, spots reflecting the crystal lattice, thereby removing the noise. The microcrystal was not totally free from distortion, and cylinders in local clusters adopted slightly different orientations. Thus, 25 hexagonal units closest to the ideal, each containing a cylinder at the center surrounded by six others, were manually selected. The averaged image was further processed to yield a perfect six-fold symmetry. These processed images, and some of the original images too, show bridges connecting cylinders, each corresponding to two pairs of N-domains, protruding from the two cylinders and contacting between them in the X-ray structure.     

Visualisation of inter loop tertiary base pairing and stacking interactions in an unusual slipped loop DNA structure

The conformation of an unusual slipped loop DNA structure exhibited by the sequence d(GAATTCCCGAATTC)₂ is determined using a combination of geometrical and molecular mechanics methods. This sequence is known to form a B-DNA-like duplex with the central non-complementary cytosines extruded into single stranded loop regions. The unusual feature is that the interior guanine does not pair with the cytosine across, instead, it pairs with the cytosine upstream by skipping two cytosines, leading to a slipped loop DNA structure with the loops staggered by two base pairs. The two loops, despite being very small, can fold across minor or major groove symmetrically or asymmetrically disposed, with one of the loop bases partially blocking the major or minor groove. Most interestingly, for certain conformations, the loop bases approach one another at close proximity so as to engage even in base pairing as well as base stacking interactions across the major groove. While such pairing and stacking are common in the tertiary folds of RNA, this is the first time that such an interaction is visualized in a DNA. This observation demonstrates that a W-C pair can readily be accomplished in a typical slipped loop structure postulated for DNA. Such tertiary loop interaction may prevent access to regulatory proteins across the major groove of the duplex DNA, thus providing a structure-function relation for the occurrence of slipped loop structure in DNA. Contribution no. 839 from this department     

Is the rigid-body assumption reasonable?: Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar

Electrostatically-driven association of proteins is important to many biological functions, and understanding which amino acid residues contribute to these interactions is crucial to protein design. Theoretical calculations that are used to elucidate the role of electrostatics in association are typically based on a single experimentally determined protein structure, while an underlying rigid-body assumption is adopted. The goal of this study was to investigate the role of conformational fluctuations on electrostatic interaction energies, as applied to the electrostatic analysis of barnase-barstar. For our calculations, we apply theoretical alanine-scan mutagenesis to introduce charge perturbations by replacing every ionizable residue with alanine, one at a time. Electrostatic clustering and free energy calculations based on the Poisson-Boltzmann method are used to evaluate the effects of each perturbation. Molecular dynamics simulations are performed for the barnase-barstar parent complex and seven experimental alanine mutations from the literature, in order to introduce relaxation before and after mutation. We discuss the effects of dynamics, in the form of pre- and post-mutation relaxation, on electrostatic clustering and free energies of association in light of experimental data. We also examine the utility of nine electrostatic similarity methods for clustering of barnase alanine-scan mutants. Our calculations suggest that the rigid-body assumption is reasonable for electrostatic calculations of barnase-barstar.     

Amphiphilic Peptide–Polymer Conjugates with Side‐Conjugation

Polymers conjugated to the exterior of a protein mediate its interactions with surroundings, enhance its processability and can be used to direct its macroscopic assemblies. Most studies to date have focused on peptide–polymer conjugates based on hydrophilic polymers. Engineering amphiphilicity into protein motifs by covalently linking hydrophobic polymers has the potential to interface peptides and proteins with synthetic polymers, organic solvents, and lipids to fabricate functional hybrid materials. Here, we synthesized amphiphilic peptide–polymer conjugates in which a hydrophobic polymer is conjugated to the exterior of a heme‐binding four‐helix bundle and systematically investigated the effects of the hydrophobicity of the conjugated polymer on the peptide structure and the integrity of the heme‐binding pocket. In aqueous solution with surfactants present, the side‐conjugated hydrophobic polymers unfold peptides and may induce an α‐helix to β‐sheet conformational transition. These effects decrease as the polymer becomes less hydrophobic and directly correlate with the polymer hydrophobicity. Upon adding organic solvent to solubilize the hydrophobic polymers, however, the deleterious effects of hydrophobic polymers on the peptide structures can be eliminated. Present studies demonstrate that protein structure is sensitive to the local environment. It is feasible to dissolve amphiphilic peptide–polymer conjugates in organic solvents to enhance their solution processability while maintaining the protein structures.

     

Statistical Thermodynamic Properties of Linear Protein Solutions

利用统计力学理论结合格点模型,讨论了链状蛋白质分子溶液的热力学性质. 结果表明,对于稀溶液来说,溶液的吉布斯函数随蛋白质浓度的增加而降低,蛋白质分子化学势随其浓度增加而升高. 还分析了蛋白质分子链长及温度对溶液吉布斯函数和蛋白质分子化学势的影响. 并且计算讨论了几种第一类抗冻蛋白的化学势.     

Approximating Data in \mathfrak{R}^{n} by a Quadratic Underestimator with Specified Hessian Minimum and Maximum Eigenvalues

The problem of approximating m data points (x _i , y _i ) in , with a quadratic function q(x, p) with s parameters, m ≥ s, is considered. The parameter vector is to be determined so as to satisfy three conditions: (1) q(x, p) must underestimate all m data points, i.e. q(x _i , p) ≤ y _i , i=1,...,m. (2) The error of the approximation is to be minimized in the L1 norm. (3) The eigenvalues of H are to satisfy specified lower and upper bounds, where H is the Hessian of q(x, p) with respect to x. This is called the Quadratic Underestimator with Bounds on Eigenvalues (QUBE) problem. An algorithm for its solution (QUBE algorithm) is given and justified, and computational results presented. The QUBE algorithm has application to finding the global minimum of a basin (or funnel) shaped function with a large number of local minima. Such problems arise in computational biology where it is desired to find the global minimum of an energy surface, in order to predict native protein-ligand docking geometry (drug design) or protein structure. Computational results for a simulated docking energy surface, with n=15, are presented. It is shown that specifying a small condition number for H improves the ability of the underestimator to correctly predict the global minimum point.