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.     

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.     

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.     

Segmentation of protein surfaces using fuzzy logic

An algorithm has been developed that can be used to divide triangulated molecular surfaces into distinct domains on the basis of physical and topographical molecular properties. Domains are defined by a certain degree of homogeneity concerning one of these properties. The method is based on fuzzy logic strategies, thus taking into consideration the smooth changes of the properties considered along complex macromolecular surfaces. Scalar qualities assigned to every node point on a triangulated surface are translated into linguistic variables, which can then be processed using a special fuzzy dissimilarity operator.Possible applications are demonstrated using surface segmentation for properties like electrostatic potential, lipophilicity and shape for the analysis of serine proteinase substrate/inhibitor specificity.     

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.     

A new technique in computer modeling of molecules with transparency effect, due to partially stripped surfaces

Conventional space filling molecular modeling in computers, using the scan method, takes considerable computer time and effort. In depicting the CPK-image on a computer screen, the hidden-point removal is the main task and on such an image, the front-line atoms hide the back-benchers and their whereabouts become completely unknown, in a given view of the picture. While in search of a simple and faster algorithm for producing surface graphics of molecules, we have developed a novel method, which is considerably faster than the conventional one and it has an interesting transparency-effect which would be useful in the various fields of molecular designs.     

The identification of complementarity of molecular surfaces using fuzzy set theory

Fuzzy logic-based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Based on these initial guesses, docking structures can be further optimized by standard technologies. In this work a simple downhill simplex method for the optimization is used. The algorithms are applied to various biomolecular complexes. For all these complexes, at least one structure was found to be in very good agreement with the experimental data.     

Trypanosoma brucei: peptide mapping of partially homologous variable surface glycoproteins.

Antigenic variation in Trypanosoma brucei is caused by amino acid sequence changes in a major surface glycoprotein. Each trypanosome may contain between 100 and 1000 genes coding for this glycoprotein. Some of these genes are members of partially homologous gene families. In addition, segments of different genes may combine to form 'hybrid' or 'mosaic' genes. Thus, surface glycoproteins exist containing varying amounts of amino acid sequence homology. For investigations of molecular mechanisms of antigenic diversity it is important to identify sub-sets of trypanosomes expressing related surface glycoproteins. We describe here a simple method based on trypanosome surface labeling followed by peptide mapping to indicate homologous peptides present in one sub-set of T. brucei surface glycoproteins.     

Study of binding between protein A and immunoglobulin G using a surface tension probe

Molecular interactions and binding are one of the most important and fundamental properties in the study of biochemical and biomedical systems. The understanding of such interactions and binding among biomolecules forms the basis for the design and processing of many biotechnological applications, such as bioseparation and immunoadsorption. In this study, we present a novel method to probe molecular interactions and binding based on surface tension measurement. This method complements conventional techniques, which are largely based on optical, spectroscopic, fluorescence polarization, chromatographic or atomic force microscopy measurements, by being definite in determining molecular binding ratio and flexible in sample preparation. Both dynamic and equilibrium (or quasi-equilibrium) information on molecular binding can be obtained through dynamic and equilibrium surface tension measurements. For an important pair of biological ligand and ligate, Protein A and immunoglobulin G (IgG), the existence of molecular interactions and the binding ratio of 1:2 have been determined unequivocally with the proposed surface tension method. These results are confirmed/supported by a mass balance calculation and spectrophotometry experiment. In addition, adsorption isotherms for Protein A and IgG separately at the air/water interface have been established with the dynamic surface tension measurements. The results show that the Langmuir isotherm equation can describe the adsorption data satisfactorily for both Protein A and IgG solutions.     

Evaluation of the contact angle from molecular simulations

An alternative method for determination of the contact angle of droplets at a solid underlay from molecular simulations is proposed. The method is based on a recently developed general method of identification the surface molecules of a molecular system with the interface of an arbitrary shape and on a subsequent parametrisation of the surface of the droplet by a smooth function. The method has been verified first by considering two artificial systems with the exactly known contact angles and then by comparison with literature data for two realistic systems.     

The beauty of molecular surfaces as revealed by self-organizing neural networks

The Kohonen neural network is a self-organizing network that can be used for the projection of the surface properties of molecules. This allows one to view properties on a molecular surface, like the electrostatic potential in a single picture. These maps are useful for the comparison of molecules and provide a new definition of molecular similarity.     

Statistical method for surface pattern-matching between dissimilar molecules: electrostatic potentials and accessible surfaces

This paper outlines a statistical method for patternmatching between surfaces and is applicable to structural and energetic patterns found on molecular surfaces. Correlation coefficients generated for the pattern match are scale invariant. Regression analysis applied to the patterns reveals the scaling and displacement relationships. The method for measuring the similarities between molecular surfaces of two dissimilar molecules held infixed orientations is given explicitly. Implicit in this procedure is a method for studying the inverse phenomenon, namely complementarity between surface parameters at a binding site and its ligand. The method has been used to assess surface differences in structural similarities generated by computer fitting and by visual comparison. Various pitfalls likely to be encountered in evaluating molecular structural similarities are noted.     

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.     

A QM/MM study of proton transport pathways in a [NiFe] hydrogenase

A theoretical QM/MM study of the [NiFe] hydrogenase from Desulfovibrio fructosovorans has been performed to investigate possible routes of proton transfer between the active site and the protein surface. We obtained the minimum energy paths, with a modified version of the nudged elastic band method, for a set of proposed pathways. The calculations were carried out for the crystallographic structure and for several structures of the protein obtained from a molecular dynamics simulation. The results show one of the studied pathways to be preferred for transport from the active site to the surface, but the preference is not so strong when transport occurs in the opposite direction.     

HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

Background  

An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated.     

Theory of cation-phospholipid-induced shape changes in a lipid bilayer couple

A quantitative model of ion binding and molecular interactions in the lipid bilayer membrane is proposed and found to be useful in examining the factors underlying such membrane characteristics as shape, sidedness, stability and vesicle size at various cation concentrations. The lipid membrane behaves as a bilayer couple whose preferential radius of curvature depends on the expansion or contraction of one monolayer relative to the other. It is proposed that molecular packing may be altered by electrostatic repulsion of adjacent like-charged phospholipid headgroups, or by bringing two headgroups closer together by divalent cation crossbridging. The surface concentrations of each type of cation-phospholipid complex can be described by simple binding equilibria and the Gouy-Chapman-Stern formulation for the surface potential in a diffuse double layer. The asymmetric distribution of acidic phospholipids in most biological membranes can account for the differential effects of identical ionic environments on either side of the bilayer. The fraction of vesicle material which tends to have a right-side-out orientation may be approximated by a normal distribution about the mean curvature. The theory generates vesicle sidedness distributions that, when fitted to experimental results from human erythrocyte membranes, provide an alternative method of estimating intrinsic cationphospholipid dissociation constants and other molecular parameters of the bilayer. The results also corroborate earlier suggestions that the Gouy-Chapman theory tends to overestimate free counter-ion concentrations at the surface under large surface potentials.     

How electronic interference can be applied in the research of the structure of small bioobjects and for "fast reading" of nucleotide sequences

A method for the study of the surface of small bioobjects, such as macromolecules and their complexes has been developed. The method is based on the phenomenon of the interference of low-energy electrons. Using the interference, it is possible to construct analogues of holograms for these bioobjects but, as distinct from optical holography, with the spatial restriction at the level of internuclear distances. The method enables one to obtain a set of holograms at different energies of electrons. The information thus obtained can suffice to determine the type of molecular groups located on the suffice of the object being examined. The method can be used, e.g., for the "fast reading" of genetic texts.