蛋白质分子表面高质量网格构建技术的研究进展

分子表面即分子边界,在一定程度上蕴含了分子的生物化学属性信息,对分子表面进行分析将有助于理解分子对接、识别和相互作用等问题。由于蛋白质分子表面的构造相对复杂,尤其是分子表面的网格化,因此寻求高效的算法构建高质量的蛋白质分子表面网格对生成光滑的分子表面、分子可视化及分子模拟都有着重要的意义。本文主要根据现有定义的蛋白质分子表面,针对近年来几种高质量分子表面网格构建的新技术进行了阐述,同时介绍了几款蛋白质分子表面可视化软件,并对它们的性能进行了简单的分析。     

The transmembrane proteins in the plasma membrane of normal human erythrocytes. Evaluation employing lactoperoxidase and proteases.

The molecular architecture of the human erythrocyte membrane has been probed using lactoperoxidase-catalyzed iodination in conjunction with Pronase hydrolysis. Resealed, hemoglobin-free ghosts were labeled at the cytoplasmic surface and the external membrane surface was subsequently digested with Pronase. Changes in size of the components labeled at the cytoplasmic surface were readily detected by sodium dodecyl sulfate gel electrophoresis. The protein 3 molecular weight class labeled at the cytoplasmic surface was extensively hydrolyzed at the external surface to produce a major 65000 molecular weight fragment and a minor 45000 molecular weight fragment. When resealed membranes were labeled on the external surface the same 65000 molecular weight labeled component is produced. These results unequivocally demonstrate that the same polypeptides in the protein 3 molecular weight class that can be labeled by lactoperoxidase at the cytoplasmic membrane surface are digested by Pronase at the external surface and are, therefore, transmembrane components. Where it is possible to label one surface of a membrane with lactoperoxidase and reseal the membrane this procedure represents an alternate method for establishing transmembrane configuration of membrane proteins.     

Characterization of surface glycoproteins of mouse lymphoid cells

We have labeled exposed surface glycoproteins of mouse lymphoid cells by the galactose oxidase-tritated sodium borohydride technique. The labeled glyco-proteins were separated by polyacrylamide slab gel electrophoresis and visualized by autoradiography (fluorography). The major thymocyte surface proteins have molecular weights of 170,000 and 125,000. Thymocytes from TL antigen-positive mouse strains showed an additional band with a molecular weight of 27,000. Highly purified T lymphocytes contain two major surface glycoproteins with molecular weights of 180,000 and 125,000. Purified B lymphocytes have one major surface glycoprotein with a molecular weight of 210,000. When T lymphocytes are stimulated in vitro by concanavalin A or phytohemag-glutinin, the major proteins characteristic of T cells are relatively weakly labeled, but new components of lower molecular weights appear on the cell surface. A similar change is seen in B lymphocytes stimulated by Escherichia coli lipopolysaccharide. T lymphoblasts isolated from mixed lymphocyte cultures show a slightly different surface glycoprotein pattern. A polypeptide with a molecular weight of 57,000, which was labeled without enzymatic treatment by tritiated sodium borohydride alone, is strongly labeled in proliferating cells.     

Molecular recognition: 3D surface structure comparison by gnomonic projection

This paper outlines a method for gnomonic projection of a molecular surface and a novel application of it to the problem of surface comparison. Semiregular arrays of points are generated by icosahedral tessellation. The surface may be the accessible surface or a chemical parameter surface such as the molecular electrostatic potential. Gnomonic projection retains the 3D characteristics of the inspection surface. Comparison of two surfaces can be achieved by statistical assessment of the pattern match. The method opens the gateway to an optimized search for pattern matches on the surfaces of dissimilar molecular structures.     

MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks

A fast algorithm for computing the solvent-accessible molecular surface area (SAS) using Boolean masks [Le Grand,S.M. and Merz,K.M.J. (1993). J. Comput. Chem., 14, 349-352) has been modified to estimate the solvent-excluded molecular surface area (SES), including contact, toroidal and re-entrant surface components. Numerical estimates of arc lengths of intersecting atomic SAS are used to estimate the toroidal surface and intersections between those arcs are used to estimate the re-entrant surface area. The new method is compared with an exact analytical method. Boolean molecular surface areas are continuous and pairwise differentiable and should be useful for molecular dynamics simulations, especially as the basis for an implicit solvent model.     

Approximation and characterization of molecular surfaces

The representation and characterization of molecular surfaces are important in many areas of molecular modeling. Parametric representations of protein molecular surfaces are a compact way to describe a surface, and are useful for the evaluation of surface properties such as the normal vector, principal curvatures, and principal curvature directions. Simplified representations of molecular surfaces are useful for efficient rendering and for the display of large-scale surface features. Several techniques for representing surfaces by expansions of spherical harmonic functions have been reported, but these techniques require that the radius function is single valued, that is, each ray from an origin inside the surface intersects the surface at one and only one point. A new technique is described that removes this limitation and can be used to compute surface shape properties. © 1993 John Wiley & Sons, Inc.     

Analytically defined surfaces to analyze molecular interaction properties

Molecular surfaces are widely used for characterizing molecules and displaying and quantifying their interaction properties. Here we consider molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density. The smoothness is advantageous for surface mapping of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defined surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, obviating the necessity to compute values of the property on an array of surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purposes. Applications to studies of protein-protein interactions are described.     

SIMS: computation of a smooth invariant molecular surface.

SIMS, a new method of calculating a smooth invariant molecular dot surface, is presented. The SIMS method generates the smooth molecular surface by rolling two probe spheres. A solvent probe sphere is rolled over the molecule and produces a Richards-Connolly molecular surface (MS), which envelops the solvent-excluded volume of the molecule. In deep crevices, Connolly's method of calculating the MS has two deficiencies. First, it produces self-intersecting parts of the molecular surface, which must be removed to obtain the correct MS. Second, the correct MS is not smooth, i.e., the direction of the normal vector of the MS is not continuous, and some points of the MS are singular. We present an exact method for removing self-intersecting parts and smoothing the singular regions of the MS. The singular MS is smoothed by rolling a smoothing probe sphere over the inward side of the singular MS. The MS in the vicinity of singularities is replaced with the reentrant surface of the smoothing probe sphere. The smoothing method does not disturb the topology of a singular MS, and the smooth MS is a better approximation of the dielectric border between high dielectric solvent and the low dielectric molecular interior. The SIMS method generates a smooth molecular dot surface, which has a quasi-uniform dot distribution in two orthogonal directions on the molecular surface, which is invariant with molecular rotation and stable under changes in the molecular conformation, and which can be used in a variety of implicit methods of modeling solvent effects. The SIMS program is faster than the Connolly MS program, and in a matter of seconds generates a smooth dot MS of a 200-residue protein. The program is available from the authors on request (see http:@femto.med.unc.edu/SIMS).     

分子表面的计算机表示

提出了一种用于生成分子光滑表面的新算法.该算法从分布在一个包含整个分子表面的椭球上的三角网络开始,逐步收缩网络直到所有的三角形最佳贴近分子表面.所使用的收缩包络椭球的技术只要稍加修改就可用于蛋白质空腔的表示.     

Transport and processing of endogenously synthesized ApoE on the macrophage cell surface

We have previously established the presence of a pool of apoE sequestered on the macrophage cell surface by demonstrating its displacement from a cell monolayer at 4 degrees C. In this series of experiments, we use a cell surface biotinylation protocol to directly quantitate apoE on the macrophage cell surface and evaluate its transport to and from this cell surface pool. In human monocyte-derived macrophages labeled to equilibrium and in a mouse macrophage cell line transfected to constitutively express human apoE3, approximately 8% of total cellular apoE was present on the surface, but only a portion of this surface pool served as a direct precursor to secreted apoE. The half-life of apoE on the macrophage cell surface was calculated to be approximately 12 min. On SDS-polyacrylamide gel electrophoresis, the apoE isolated from the surface fraction of cells labeled to equilibrium migrated in an isoform pattern distinct from that observed from the intracellular fraction, with the surface fraction migrating predominantly in a higher molecular weight isoform. Pulse labeling experiments demonstrated that newly synthesized apoE reached the cell surface by 10 min but was predominantly in a low molecular weight isoform. There was also a lag between appearance of apoE on the cell surface and its appearance in the medium. Biotinylated apoE, which accumulated in the medium, even from pulse labeled cells, was predominantly in the high molecular weight isoform. Additional experiments demonstrated that low molecular weight apoE present on the cell surface was modified to higher molecular weight apoE by the addition of sialic acid residues prior to secretion and that this conversion was inhibited by brefeldin A. These results demonstrate an unexpected complexity in the transport and cellular processing of macrophage cell surface apoE. Factors that modulate the size and turnover of the cell surface pool of apoE in the macrophage remain to be identified and investigated.     

Molecular recognition via face center representation of a molecular surface

While docking methodologies are now frequently being developed, a careful examination of the molecular surface representation, which necessarily is employed by them, is largely overlooked. There are two important aspects here that need to be addressed: how the surface representation quantifies surface complementarity, and whether a minimal representation is employed. Although complementarity is an accepted concept regarding molecular recognition, its quantification for computation is not trivial, and requires verification. A minimal representation is important because docking searches a conformational space whose extent and/ or dimensionality grows quickly with the size of surface representation, making it especially costly with big molecules, imperfect interfaces, and changes of conformation that occur in binding. It is essential for a docking methodology to establish that it employs an accurate, concise molecular surface representation.Here we employ the face center representation of molecular surface, developed by Lin et al.,¹ to investigate the complementarity of molecular interface. We study a wide variety of complexes: protein/small ligand, oligomeric chain-chain interfaces, proteinase/protein inhibitors, antibody/antigen, NMR structures, and complexes built from unbound, separately solved structures. The complementarity is examined at different levels of reduction, and hence roughness, of the surface representation, from one that describes subatomic details to a very sparse one that captures only the prominent features on the surface. Our simulation of molecular recognition indicates that in all cases, quality interface complementarity is obtained. We show that the representation is powerful in monitoring the complementarity either in its entirety, or in selected subsets that maintain a fraction of the face centers, and is capable of supporting molecular docking at high fidelity and efficiency. Furthermore, we also demonstrate that the presence of explicit hydrogens in molecular structures may not benefit docking, and that the different classes of protein complexes and may hold slightly different degrees of interface complementarity.     

Ganglioside GD3 lactones: polar head group mediated control of the intermolecular organization

The individual properties and intermolecular organization of ganglioside GD3 and of two of its lactone forms (GD3Lactone I and GD3Lactone II) were studied in lipid monolayers. The formation of the first lactone ring in GD3Lactone I eliminates one negative charge and leads to a decrease of the molecular area at all surface pressures. The intermolecular dispersion energy and collapse pressure are higher in GD3Lactone I compared to those in the parent GD3. The surface potential per unit of molecular surface density and the resultant molecular dipole moment are increased in GD3Lactone I with respect to those in GD3 at comparable values of molecular area. In GD3Lactone I the molecular parameters suggest an oligosaccharide chain oriented similarly to that of GD3. On the average, this is perpendicular to the surface, and the resultant polar head-group dipole moment points away from the interface. In GD3Lactone II the negative charges are eliminated, resulting in considerably larger molecular areas than for GD3 and GD3Lactone I at all pressures. The intermolecular dispersion energy of GD3Lactone II is also greatly diminished and the collapse pressure is further increased compared to those of GD3Lactone I. However, the surface potential per unit molecular surface density and the resultant molecular dipole moment of GD3Lactone II are higher than in GD3 Lactone I at similar values of molecular areas. This is probably due to a positive polar head-group dipole moment contribution induced by the additional lactone ring in GD3Lactone II. These changes result from a distorted conformation of the oligosaccharide chain owing to the presence of fused carbohydrate rings which require a greater intermolecular spacing compared to GD3 and GD3Lactone I.     

Protein Molecular Surface Mapped at Different Geometrical Resolutions

Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.     

Molecular surface representations by sparse critical points

We have defined a molecular surface representation that describes precisely and concisely the complete molecular surface. The representation consists of a limited number of critical points disposed at key locations over the surface. These points adequately represent the shape and the important characteristics of the surface, despite the fact that they are modest in number. We expect the representation to be useful in areas such as molecular recognition and visualization. In particular, using this representation, we are able to achieve accurate and efficient protein–protein and protein–small molecule docking. © 1994 John Wiley & Sons, Inc.     

Conformational changes in single carboxymethylcellulose chains on a highly oriented pyrolytic graphite surface under different salt conditions

Conformational changes in individual carboxymethylcellulose (CMC) chains deposited on a highly oriented pyrolytic graphite (HOPG) surface were investigated by atomic force microscopy (AFM). A small amount of CMC solution with various salt concentrations was deposited onto the HOPG surface. The CMC molecular chains adsorbed onto the HOPG surface were clearly visualized using tapping-mode AFM under ambient conditions, as compared with those on a hydrophilic mica surface. Each CMC chain was distinguishable at the molecular level based on the vertical profiles of the AFM images, and probably aligned along the HOPG crystal lattice. Higher NaCl concentrations brought about dramatic conformational changes from aligned single chains to globular aggregates via the molecular network structure only on the HOPG surface through electrostatic screening of the CM groups. Although CMC is a water-soluble hydrophilic polyelectrolyte, some interaction, possibly due to a CH-pi bonding between the glucopyranosic axial plane of CMC and the aromatic rings of HOPG, is considered to be effective and dominant for the unique molecular attachment. These phenomena would imply the potential use of HOPG as a substrate for not only molecular imaging, but also for nano-scale morphological control of cellulosic polymers and other structural polysaccharides.     

The ion channel switch biosensor

A biosensor technology is described which provides a direct measurement for functional molecular interactions, at the surface of a tethered bilayer membrane, through the electrical transduction of chemically modified ion-channels. High sensitivity of analyte detection is achieved due to the large flux of ions transmitted through the ion channel. The biomimetic sensor surface allows the molecular recognition to be measured in complex biological matrices (such as blood and sera) without compromising sensitivity. We have used the sensor for activity and concentration measurements for a range of analytes, which include bacteria, DNA, proteins and drugs. We have a quantitative model for the biosensor performance which is described by three-dimensional molecular interactions with the membrane surface and two-dimensional molecular interactions within the tethered bilayer.     

Surface rheological properties of hyaluronic acid solutions

Using an oscillating ring surface rheometer, surface shear rheological studies of hyaluronic acid solutions at physiological pH have demonstrated the elastico-viscous nature of the surface films. The properties of these surface films change with time and are shown to be related to bulk concentration, ionic strength and pH. This ageing behaviour can be explained on the basis of molecular conformational changes and molecular segmental kinetics. The results are discussed in relation to the postulated function of hyaluronic acid in synovial fluid.