Building self-avoiding lattice models of proteins using a self-consistent field optimization

We present an algorithm to build self-avoiding lattice models of chain molecules with low RMS deviation from their actual 3D structures. To find the optimal coordinates for the lattice chain model, we minimize a function that consists of three terms: (1) the sum of squared deviations of link coordinates on a lattice from their off-lattice values, (2) the sum of “short-range” terms, penalizing violation of chain connectivity, and (3) the sum of “long-range” repulsive terms, penalizing chain self-intersections. We treat this function as a chain molecule “energy” and minimize it using self-consistent field (SCF) theory to represent the pairwise link repulsions as 3D fields acting on the links. The statistical mechanics of chain molecules enables computation of the chain distribution in this field on the lattice. The field is refined by iteration to become self-consistent with the chain distribution, then dynamic programming is used to find the optimal lattice model as the “lowest-energy” chain pathway in this SCF. We have tested the method on one of the coarsest (and most difficult) lattices used for model building on proteins of all structural types and show that the method is adequate for building self-avoiding models of proteins with low RMS deviations from the actual structures. © 1996 Wiley-Liss, Inc.     

Molecular structure of bacterial endotoxin (Escherichia coli Re lipopolysaccharide): implications for formation of a novel heterogeneous lattice structure

Analyses of crystals of Escherichia coli Re lipopolysaccharide (LPS) formed after storage in 1% triethylamine indicate that the LPS molecules are assembled to form a monolayered structure consisting of a novel heterogeneous lattice structure, the greater part of which is occupied by one kind of lattice (lattice I), corresponding to the acyl chain portion of lipid A, and the remainder is occupied by the other kind of lattice (lattice II), corresponding to the 3-deoxy-Dmanno-octulosonic acid (dOclA) dimer and the N-acetylglucosamine disaccharide of lipid A. X-ray diffraction reveals that the type of cell is monoclinic (a = 5.53 A, b = 27.2 A, c = 6.47 A, alpha = 90 degrees, beta = 125.8 degrees, gamma = 90 degrees ). Atomic force microscopy shows that crystals consist of multiple layers; the thickness of a layer corresponds to the b-axis value, and two types of surface topographies are visualized. One, regarded as the view onto the acyl chain ends, is two-dimensional arrays of oval bodies that constitute the lattice, with the lattice constants corresponding to the a- and c-axes and the angle of beta (lattice I). The other, regarded as the view onto the dOclA dimers, is two-dimensional arrays of dromedary-back-like bodies that constitute the lattice with axes of 9.0 and 10.7 A and the angle of 65 degrees formed by both axes (lattice II). Based on these results, we present the molecular model of E. coli Re LPS.     

利用粒子群算法在菱形网格上预测蛋白质结构

本文在菱形网格上研究讨论了二维HP模型。首先,将蛋白质结构预测问题转化成一个数学问题,并简化成氨基酸序列中每个氨基酸与网格格点的匹配问题。为了解决这个数学问题,我们改进并扩展了经典的粒子群算法。为了验证算法和模型的有效性,我们对一些典型的算例进行数值模拟。通过与方格网上得到的蛋白质构象进行比较,菱形网上的蛋白质构象更自然,更接近真实。我们进一步比较了菱形网格上的紧致构象和非紧致构象。结果显示我们的模型和算法在菱形网格上预测氨基酸序列的蛋白质结构是有效的有意义的。     

An introduction to niche construction theory

Niche construction refers to the modification of selective environments by organisms. Theoretical and empirical studies of niche construction are increasing in importance as foci in evolutionary ecology. This special edition presents theoretical and empirical research that illustrates the significance of niche construction to the field. Here we set the scene for the following papers by (1) discussing the history of niche construction research, (2) providing clear definitions that distinguish niche construction from related concepts such as ecosystem engineering and the extended phenotype, (3) providing a brief summary of the findings of niche construction research, (4) discussing the contribution of niche construction and ecological inheritance to (a) expanded notions of inheritance, and (b) the extended evolutionary synthesis, and (5) briefly touching on some of the issues that underlie the controversies over niche construction.     

Structure of the crystalline bilayer in the subgel phase of dipalmitoylphosphatidylglycerol

The structure of the subgel phase of dipalmitoylphosphatidylglycerol (DPPG) has been analyzed by X-ray diffraction techniques. Diffraction recorded from highly oriented DPPG specimens in the subgel phase extends to 2-A resolution. There are sharp lamellar reflections on the meridian, and other reflections lie on a series of wide-angle lattice lines parallel to the meridian and crossing the equator in the range of 8-2 A. The wide-angle lattice lines consist of radially sharp reflections centered on the equator of the X-ray film and also a series of broader, off-equatorial maxima. The lattice lines indicate that the DPPG molecules in each bilayer crystallize in a two-dimensional oblique lattice with dimensions a = 5.50 A, b = 7.96 A, and gamma = 100.5 degrees. These oblique lattices are not regularly aligned from bilayer to bilayer. Analysis of the lamellar diffraction shows that the bilayer has about the same thickness in the subgel and gel (L beta') phases. In the direction normal to the hydrocarbon chains, the chains are significantly closer together in the subgel phase as compared to the normal L beta' gel phase but have about the same separation as the chains in polyethylene and the crystalline n-alkanes. The bilayer thickness, area per lipid molecule, and intensity distribution along the lattice lines all indicate that in the subgel phase the hydrocarbon chains are tilted between 30 and 35 degrees from the normal to the bilayer plane.(ABSTRACT TRUNCATED AT 250 WORDS)     

Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamics

A simple coarse-grained model of mucus structure and dynamics is proposed and evaluated. The model is based on simple cubic, face-centered lattice representation. Mucins are simulated as lattice chains in which each bead of the model chains represents a mucin domain, equivalent to its Kuhn segment. The remaining lattice sites are considered to be occupied by the solvent. Model mucins consist of three types of domains: polar (glycosylated central segments), hydrophobic, and cysteine-rich, located at the terminal part of the mucin chains. The sequence of these domains mimics the sequence of real mucins. Static and dynamic properties of the system were studied by means of Monte Carlo dynamics. It was shown that the model system undergoes sol-gel transition and that the interactions between hydrophobic domains are responsible for the transition and characteristic properties of the dynamic network in the gel phase. Cysteine-rich domains are essential for frictional properties of the system. Structural and dynamic properties of the model mucus observed in simulations are in qualitative agreement with known experimental facts and provide mechanistic explanation of complex properties of real mucus.     

A hierarchical method for generating low-energy conformers of a protein-ligand complex

A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented. Proteins 33:475–495, 1998. © 1998 Wiley-Liss, Inc.     

Lipopeptides as anti-infectives: a practical perspective

Lipopeptide antibiotics represent an old class of antibiotics that were discovered over 50 years ago, which includes the old polymyxins but also new entries, such as the recently approved daptomycin. They generally consist of a hydrophilic cyclic peptide portion attached to a fatty acid chain which facilitates insertion into the lipid bilayer of bacterial membranes. This review presents an overview of this class of antibiotics, focusing on their therapeutic applications and putting particular emphasis on chemical modifications introduced to improve their activity.     

Rhodopsins build up the birefringent bodies of the dinoflagellate Oxyrrhis marina

The ultrastructure of the birefringent bodies of the dinoflagellate Oxyrrhis marina was investigated by transmission electron microscopy. Ultrathin sectioning revealed that the bodies consist of highly ordered and densely packed lamellae, which show a regular striation along their longitudinal axis. A lattice distance of 6.1 nm was measured for the densely packed lamellae by FFT (Fast Fourier Transformation) analysis. In addition, a rather faint and oblique running striation was registered. Lamellae sectioned rather oblique or almost close to the surface show a honeycombed structure with a periodicity of 7.2–7.8 nm. Freeze-fracture transmission electron microscopy revealed that the lamellae are composed of highly ordered, crystalline arrays of particles. Here, FFT analysis resulted in lattice distances of 7.0–7.6 nm. Freeze-fracture transmission electron microscopy further revealed that the bodies remained intact after cell rupture followed by ascending flotation of the membrane fractions on discontinuous sucrose gradients. The birefringent bodies most likely are formed by evaginations of membranes, which separate the cytoplasm from the food vacuoles. Distinct, slightly reddish-colored areas, which resembled the birefringent bodies with respect to size and morphology, were registered by bright field light microscopy within Oxyrrhis marina cells. An absorbance maximum at 540 nm was registered for these areas, indicating that they are composed of rhodopsins. This was finally proven by immuno-transmission electron microscopy, as antisera directed against the C-terminal amino acid sequences of the rhodopsins AEA49880 and ADY17806 intensely immunolabeled the birefringent bodies of Oxyrrhis marina.

     

Construction of hybrid photosynthetic units using peripheral and core antennae from two different species of photosynthetic bacteria: detection of the energy transfer from bacteriochlorophyll a in LH2 to bacteriochlorophyll b in LH1

Typical purple bacterial photosynthetic units consist of supra-molecular arrays of peripheral (LH2) and core (LH1-RC) antenna complexes. Recent atomic force microscopy pictures of photosynthetic units in intact membranes have revealed that the architecture of these units is variable (Scheuring et al. (2005) Biochim Bhiophys Acta 1712:109–127). In this study, we describe methods for the construction of heterologous photosynthetic units in lipid-bilayers from mixtures of purified LH2 (from Rhodopseudomonas acidophila) and LH1-RC (from Rhodopseudomonas viridis) core complexes. The architecture of these reconstituted photosynthetic units can be varied by controlling ratio of added LH2 to core complexes. The arrangement of the complexes was visualized by electron-microscopy in combination with Fourier analysis. The regular trigonal array of the core complexes seen in the native photosynthetic membrane could be regenerated in the reconstituted membranes by temperature cycling. In the presence of added LH2 complexes, this trigonal symmetry was replaced with orthorhombic symmetry. The small lattice lengths for the latter suggest that the constituent unit of the orthorhombic lattice is the LH2. Fluorescence and fluorescence-excitation spectroscopy was applied to the set of the reconstituted membranes prepared with various proportions of LH2 to core complexes. Remarkably, even though the LH2 complexes contain bacteriochlorophyll a, and the core complexes contain bacteriochlorophyll b, it was possible to demonstrate energy transfer from LH2 to the core complexes. These experiments provide a first step along the path toward investigating how changing the architecture of purple bacterial photosynthetic units affects the overall efficiency of light-harvesting.     

Bacterial and Archaeal S-Layers as a Subject of Nanobiotechnology

Many bacteria and archaea have a crystalline surface layer (S-layer), which overlies the cell envelope. S-layers each consist of one protein or glycoprotein species. Protein subunits of the S-layer noncovalently interact with each other and with the underlying cell-envelope component. On average, the S-layer lattice has pores of 2–6 nm and is 5–10 nm high. Isolated S-layer proteins recrystallize to form two-dimensional crystalline structures in solution, on a solid support, and on planar lipid membranes. Owing to this unique property, S-layers have a broad range of applications. This review focuses on the structural features and applications of S-layers and their proteins, with special emphasis on their use in nanobiotechnology.     

Wall architecture with high porosity is established at the tip and maintained in growing pollen tubes of Nicotiana tabacum

A major question in pollen tube growth in planta remains: do the pollen tube walls form a barrier to interaction with the environment? Using cryo‐FESEM, we directly assessed the 3D construction and porosity of tobacco pollen tube walls. Fractured mature primary walls showed a 40–50 nm spaced lattice of continuous fibers interconnected by short rods in the primary wall. These observations agree with TEM observations of sectioned walls. In the secondary callose wall, for which no structure is visible using TEM, cryo‐FESEM also revealed a 50 nm lattice consisting of longer fibers, approximately 10–15 nm wide, with rod‐like, thinner interconnections at angles of approximately 90° with the longer fibers. Such architecture may reflect functional needs with respect to porosity and mechanical strength. The wall does not form a mechanical barrier to interaction with the environment and is gained at low cost. Cryo‐FESEM additionally revealed another special feature of the wall: the tubes were tiled with scales or rings that were highly conspicuous after pectin extraction with EDTA. These rings cause the typical banding patterns of pectin that are commonly seen in pollen tubes during oscillatory growth, as confirmed by staining with toluidine blue as well as by DIC microscopy. Growth analysis by VEC‐LM showed that the ring‐ or scale‐like structures of the primary wall consist of material deposited prior to the growth pulses. The alternating band pattern seen in the callose wall is probably imposed by constrictions resulting from the rings of the primary wall.     

Application of the synthetic jet concept to low Reynolds number biosensor microfluidic flows for enhanced mixing: a numerical study using the lattice Boltzmann method

The concept of macro scale synthetic jets has been applied to the low Reynolds number (Re=10), two-dimensional channel flows which may be found in biosensor microfluidic systems. The current numerical investigation utilizes a hybrid approach of the lattice Boltzmann (LB) method for flow field computations and a finite-difference, convection-diffusion equation for passive scalar transport. The study presents the modified main channel flow results for various wall jet geometries (derived from synthetic jets), jet inlet conditions, scaling issues and Reynolds numbers. The results indicate limited effects due to jet cavity-slot geometry, and that the forced jet imparts momentum to the channel flow thus enhancing fluid mixing.     

Hierarchical assembly of the siliceous skeletal lattice of the hexactinellid sponge Euplectella aspergillum

Despite its inherent mechanical fragility, silica is widely used as a skeletal material in a great diversity of organisms ranging from diatoms and radiolaria to sponges and higher plants. In addition to their micro- and nanoscale structural regularity, many of these hard tissues form complex hierarchically ordered composites. One such example is found in the siliceous skeletal system of the Western Pacific hexactinellid sponge, Euplectella aspergillum. In this species, the skeleton comprises an elaborate cylindrical lattice-like structure with at least six hierarchical levels spanning the length scale from nanometers to centimeters. The basic building blocks are laminated skeletal elements (spicules) that consist of a central proteinaceous axial filament surrounded by alternating concentric domains of consolidated silica nanoparticles and organic interlayers. Two intersecting grids of non-planar cruciform spicules define a locally quadrate, globally cylindrical skeletal lattice that provides the framework onto which other skeletal constituents are deposited. The grids are supported by bundles of spicules that form vertical, horizontal and diagonally ordered struts. The overall cylindrical lattice is capped at its upper end by a terminal sieve plate and rooted into the sea floor at its base by a flexible cluster of barbed fibrillar anchor spicules. External diagonally oriented spiral ridges that extend perpendicular to the surface further strengthen the lattice. A secondarily deposited laminated silica matrix that cements the structure together additionally reinforces the resulting skeletal mass. The mechanical consequences of each of these various levels of structural complexity are discussed.     

Low resolution structure of microtubules in solution. Synchrotron X-ray scattering and electron microscopy of taxol-induced microtubules assembled from purified tubulin in comparison with glycerol and MAP-induced microtubules.

The structure of microtubules has been characterized to 3 nm resolution employing time-resolved X-ray scattering. This has revealed detailed structural features of microtubules not observed before in solution. The polymerization of highly purified tubulin, induced by the antitumour drug taxol, has been employed as a microtubule model system. This assembly reaction requires Mg2+, is optimal at a 1:1 taxol to tubulin heterodimer molar ratio, proceeds with GTP or GDP and is intrinsically reversible. The X-ray scattering profiles are consistent with identical non-globular alpha and beta-tubulin monomers ordered within the known helical surface lattice of microtubules. Purified tubulin-taxol microtubules have a smaller mean diameter (approx. 22 nm) than those induced by microtubule associated proteins or glycerol (approx. 24 nm), but nearly identical wall substructure to the resolution of the measurements. This is because the majority of the former consist of only 12 protofilaments instead of the typical 13 protofilaments, as confirmed by electron microscopy of thin-sectioned, negatively stained and ice-embedded taxol microtubules. It may be concluded that taxol induces a slight reduction of the lateral contact curvature between tubulin monomers. The main fringe pattern observed in cryo-electron micrographs is consistent with a simple 12 protofilament 3-start skewed lattice model. Cylindrical closure of this lattice can be achieved by tilting the lattice 0.8 degrees with respect to the microtubule axis. The closure implies a discontinuity in the type of lateral contacts between the tubulin monomers (regardless of whether these are of the -alpha-beta- or the -alpha-alpha-/-beta-beta- type), which indicates that lateral contacts and the subunit specificity of taxol binding are, to a large degree, equivalent.     

On lattice protein structure prediction revisited

Protein structure prediction is regarded as a highly challenging problem both for the biology and for the computational communities. In recent years, many approaches have been developed, moving to increasingly complex lattice models and off-lattice models. This paper presents a Large Neighborhood Search (LNS) to find the native state for the Hydrophobic-Polar (HP) model on the Face-Centered Cubic (FCC) lattice or, in other words, a self-avoiding walk on the FCC lattice having a maximum number of H-H contacts. The algorithm starts with a tabu-search algorithm, whose solution is then improved by a combination of constraint programming and LNS. The flexible framework of this hybrid algorithm allows an adaptation to the Miyazawa-Jernigan contact potential, in place of the HP model, thus suggesting its potential for tertiary structure prediction. Benchmarking statistics are given for our method against the hydrophobic core threading program HPstruct, an exact method which can be viewed as complementary to our method.     

A novel retrieval system for nearly complete microbial genomic fragments from soil samples

The construction of a complex genomic library is one of the comprehensive ways to study a complex bacterial community and to access the variety of metabolic pathways present in the rich soil environment. In this report, we developed a new protocol whereby we are able to retrieve nearly complete microbe genomic fragments from soil samples, which are employed to generate a metagenomic library for visualizing the basic scaffolding of the soil microbial community. The use of direct cell lysis within soil-embedded agarose plugs, along with a double-size selection, enabled us to successfully isolate pure and high-molecular weight DNA (0.1-1 Mb) without the need for any further purification. A metagenomic library containing 1.2 Gbp of DNA in total was constructed. Furthermore, analysis of the microbial community structure using 16S rDNA partial sequences found the dominant phylotypes to consist of alpha-Proteobacteria and Actinobacteria, which are similar to those seen in forest and agricultural soils, and numerous uncultured microbes from a wide variety of bacterial taxa as well. In conclusion, this study presents a novel protocol for generating a metagenomic library that carries much larger and diverse DNA fragments from soil bacteria that will be applied for the reconstruction of soil microbial genomes and the discovery of novel habitat-specific pathways.     

A kinetic lattice model of the chain-melting phase transition in lipid membrane: its experimental calibration and physiological implications

A kinetic lattice model of chain-melting phase transition has been developed. Its time scale has been calibrated with the acoustic relaxation spectroscopic data. The model presents a tool for the analysis and predictions of kinetic features of those physiological processes in biological membranes whose mechanism is based on the phase transition in the lipid component. It has been shown that the phase-transitional mechanism can provide a high rate of synaptic exocytosis known for the fastest synapses in the central nervous system. It was also demonstrated that this mechanism can serve as an essential factor of synaptic plasticity.     

Evidence that the N-terminal part of the S-layer protein from Bacillus stearothermophilus PV72/p2 recognizes a secondary cell wall polymer.

The S-layer of Bacillus stearothermophilus PV72/p2 shows oblique lattice symmetry and is composed of identical protein subunits with a molecular weight of 97,000. The isolated S-layer subunits could bind and recrystallize into the oblique lattice on native peptidoglycan-containing sacculi which consist of peptidoglycan of the A1gamma chemotype and a secondary cell wall polymer with an estimated molecular weight of 24,000. The secondary cell wall polymer could be completely extracted from peptidoglycan-containing sacculi with 48% HF, indicating the presence of phosphodiester linkages between the polymer chains and the peptidoglycan backbone. The cell wall polymer was composed mainly of GlcNAc and ManNAc in a molar ratio of 4:1, constituted about 20% of the peptidoglycan-containing sacculus dry weight, and was also detected in the fraction of the S-layer self-assembly products. Extraction experiments and recrystallization of the whole S-layer protein and proteolytic cleavage fragments confirmed that the secondary cell wall polymer is responsible for anchoring the S-layer subunits by the N-terminal part to the peptidoglycan-containing sacculi. In addition to this binding function, the cell wall polymer was found to influence the in vitro self-assembly of the guanidinium hydrochloride-extracted S-layer protein. Chemical modification studies further showed that the secondary cell wall polymer does not contribute significant free amino or carboxylate groups to the peptidoglycan-containing sacculi.     

Semantics of case

This paper presents a framework which connects case assignment with the semantics of argument realization. Broad notions of agency and affectedness are decomposed into more fine-grained semantic properties, loosely based on Dowty??s Proto-Role theory, but conceived in terms of privative opposition and organized into a lattice. This lattice provides a semantic space of participant properties and supports defining hierarchical relations among participant types, interpreted as semantic prominence, as well as topological relations such as ??closeness??, interpreted as semantic similarity between participant types. Cases are defined as connected regions of this space, relating a given case to a structured set of semantic properties. A case system is represented as a semantic system, which embodies oppositions and contrasts, and operates against the backdrop of the general semantics of argument realization, where one can define notions such as maximal agents and maximal patients and represent generalizations from the research on transitivity. Core case markers (e.g. ergative, accusative) are represented as subspaces of the lattice spreading outwards from the maximal agent and maximal patient nodes of the lattice. Case alternations arise when the subspace of the lattice delimited by a predicate??s entailments for an argument is partitioned by different cases, exemplified with the genitive/accusative alternation in Russian occurring with direct objects of certain intensional predicates. This method also provides a treatment of case polysemy, viz. a single case subsuming multiple uses, by relating the diverse uses at the more abstract semantic level of the case??s region on the lattice, demonstrated with non-canonical uses of the dative.