scholarly journals Tertiary Structure of Bacterial Murein: the Scaffold Model

2003 ◽  
Vol 185 (11) ◽  
pp. 3458-3468 ◽  
Author(s):  
Boris A. Dmitriev ◽  
Filip V. Toukach ◽  
Klaus-Jürgen Schaper ◽  
Otto Holst ◽  
Ernst T. Rietschel ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Length Distribution ◽  
Molecular Architecture ◽  
Chain Length Distribution ◽  
Division Plane ◽  
Glycan Chain ◽  
Planar Network

ABSTRACT Although the chemical structure and physical properties of peptidoglycan have been elucidated for some time, the precise three-dimensional organization of murein has remained elusive. Earlier published computer simulations of the bacterial murein architecture modeled peptidoglycan strands in either a regular (D. Pink, J. Moeller, B. Quinn, M. Jericho, and T. Beveridge, J. Bacteriol. 182: 5925-5930, 2000) or an irregular (A. Koch, J. Theor. Biol. 204: 533-541, 2000) parallel orientation with respect to the plasma membrane. However, after integrating published experimental data on glycan chain length distribution and the degree of peptide side chain cross-linking into this computer simulation, we now report that the proposed planar network of murein appears largely dysfunctional. In contrast, a scaffold model of murein architecture, which assumes that glycan strands extend perpendicularly to the plasma membrane, was found to accommodate published experimental evidence and yield a viable stress-bearing matrix. Moreover, this model is in accordance with the well-established principle of murein assembly in vivo, i.e., sequential attachment of strands to the preexisting structure. For the first time, the phenomenon of division plane alternation in dividing bacteria can be reconciled with a computer model of the molecular architecture of murein.

scholarly journals Protein Folding: Search for Basic Physical Models

2003 ◽  
Vol 3 ◽  
pp. 623-635 ◽  
Author(s):  
Ivan Y. Torshin ◽  
Robert W. Harrison
Keyword(s):  
Protein Folding ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Physical Models ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Linear Sequence ◽  
Physical Forces

How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context ofin vivoprotein folding (which has been studied only for a few proteins), the roles of the fundamental physical forces in thein vitrofolding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces). Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

scholarly journals Substructure of crystalline peroxisomes in methanol-grown Hansenula polymorpha: evidence for an in vivo crystal of alcohol oxidase.

1981 ◽  
Vol 1 (10) ◽  
pp. 949-957 ◽  
Author(s):  
M Veenhuis ◽  
W Harder ◽  
J P van Dijken ◽  
F Mayer
Keyword(s):  
Osmotic Shock ◽  
Hansenula Polymorpha ◽  
Three Dimensional ◽  
Alcohol Oxidase ◽  
Molecular Architecture ◽  
Three Dimensional Model ◽  
Structural Element ◽  
Free Mobility ◽  
Crystalline Matrix

The substructural organization of completely crystalline peroxisomes present in Hansenula polymorpha cells grown under methanol limitation in a chemostat was investigated by different cytochemical and ultrastructural techniques. Time-dependent cytochemical staining experiments indicated that activities of the two main constituents of these organelles, namely, alcohol oxidase and catalase, were present throughout the crystalline matrix. Catalase was completely removed from isolated peroxisomes by osmotic shock treatment. After such treatment, the ultrastructure of the crystalline matrix of the organelles remained virtually intact. Because alcohol oxidase activity was still present in this matrix, it was concluded that alcohol oxidase protein is the only structural element of the peroxisomal crystalloids. The molecular architecture of the crystalloids was investigated in ultrathin cryosections which permitted recognition of individual molecules in the crystalline matrix. Depending on the plane of sectioning, different crystalline patterns were observed. Tilting experiments indicated that these images were caused by superposition of octameric alcohol oxidase molecules arranged in a tetragonal lattice. A three-dimensional model of the crystalloid is presented. The repeating unit of this structure is composed of four alcohol oxidase molecules. The crystalloid represents an open structure, which may explain the observed free mobility of catalase molecules.

scholarly journals Natural hybrid silica/protein superstructure at atomic resolution

2020 ◽  
Vol 117 (49) ◽  
pp. 31088-31093
Author(s):  
Stefan Görlich ◽  
Abisheik John Samuel ◽  
Richard Johannes Best ◽  
Ronald Seidel ◽  
Jean Vacelet ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Three Dimensional ◽  
Inorganic Materials ◽  
Atomic Resolution ◽  
Axial Filament ◽  
X Ray Crystallography ◽  
Organic Hybrid ◽  
Hybrid Silica ◽  
Transmission Electron

Formation of highly symmetric skeletal elements in demosponges, called spicules, follows a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by a highly ordered proteinaceous scaffold, the axial filament. The enzymatically active proteins, silicateins, are assembled into a slender hybrid silica/protein crystalline superstructure that directs the morphogenesis of the spicules. Furthermore, silicateins are known to catalyze the formation of a large variety of other technologically relevant organic and inorganic materials. However, despite the biological and biotechnological importance of this macromolecule, its tertiary structure was never determined. Here we report the atomic structure of silicatein and the entire mineral/organic hybrid assembly with a resolution of 2.4 Å. In this work, the serial X-ray crystallography method was successfully adopted to probe the 2-µm-thick filaments in situ, being embedded inside the skeletal elements. In combination with imaging and chemical analysis using high-resolution transmission electron microscopy, we provide detailed information on the enzymatic activity of silicatein, its crystallization, and the emergence of a functional three-dimensional silica/protein superstructure in vivo. Ultimately, we describe a naturally occurring mineral/protein crystalline assembly at atomic resolution.

scholarly journals The cellular level of O-antigen polymerase Wzy determines chain length regulation by WzzB and WzzpHS-2 in Shigella flexneri 2a

Microbiology ◽  
2009 ◽  
Vol 155 (10) ◽  
pp. 3260-3269 ◽  
Author(s):  
Javier A. Carter ◽  
Juan C. Jiménez ◽  
Mercedes Zaldívar ◽  
Sergio A. Álvarez ◽  
Cristina L. Marolda ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Chain Length ◽  
Shigella Flexneri ◽  
Length Distribution ◽  
Direct Interaction ◽  
Cellular Level ◽  
Chain Length Distribution ◽  
Inducible Promoters ◽  
O Antigen

The lipopolysaccharide O antigen of Shigella flexneri 2a has two preferred chain lengths, a short (S-OAg) composed of an average of 17 repeated units and a very long (VL-OAg) of about 90 repeated units. These chain length distributions are controlled by the chromosomally encoded WzzB and the plasmid-encoded WzzpHS-2 proteins, respectively. In this study, genes wzzB, wzz pHS-2 and wzy (encoding the O-antigen polymerase) were cloned under the control of arabinose- and rhamnose-inducible promoters to investigate the effect of varying their relative expression levels on O antigen polysaccharide chain length distribution. Controlled expression of the chain length regulators wzzB and wzz pHS-2 revealed a dose-dependent production of each modal length. Increase in one mode resulted in a parallel decrease in the other, indicating that chain length regulators compete to control the degree of O antigen polymerization. Also, when expression of the wzy gene is low, S-OAg but not VL-OAg is produced. Production of VL-OAg requires high induction levels of wzy. Thus, the level of expression of wzy is critical in determining O antigen modal distribution. Western blot analyses of membrane proteins showed comparable high levels of the WzzB and WzzpHS-2 proteins, but very low levels of Wzy. In vivo cross-linking experiments and immunoprecipitation of membrane proteins did not detect any direct interaction between Wzy and WzzB, suggesting the possibility that these two proteins may not interact physically but rather by other means such as via translocated O antigen precursors.

scholarly journals Increased Glycan Chain Length Distribution and Decreased Susceptibility to Moenomycin in a Vancomycin-Resistant Staphylococcus aureus Mutant

2002 ◽  
Vol 46 (1) ◽  
pp. 75-81 ◽  
Author(s):  
Hitoshi Komatsuzawa ◽  
Kouji Ohta ◽  
Sakuo Yamada ◽  
Kerstin Ehlert ◽  
Harald Labischinski ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Chain Length ◽  
Length Distribution ◽  
Reversed Phase ◽  
Chain Length Distribution ◽  
Penicillin Binding Proteins ◽  
Glycan Chain ◽  
Peptidoglycan Hydrolases ◽  
Vancomycin Resistant

ABSTRACT A vancomycin-resistant Staphylococcus aureus mutant, COL-VR1 (MIC, 16 μg/ml), was isolated from methicillin-resistant S. aureus COL by exposure to vancomycin. COL-VR1 also showed decreased susceptibility to teicoplanin (8-fold), methicillin (2-fold), macarbomycin (8-fold), and moenomycin (16-fold). Macarbomycin and moenomycin are thought to directly inhibit transglycosylase activity. Characterization of the mutant revealed a thickened cell wall and suppression of penicillin-induced lysis, although the amounts of the five penicillin-binding proteins (PBPs 1, 2, 3, 4, and 2′) and the profiles of peptidoglycan hydrolases were not altered. Analysis of muropeptide profile and glycan chain length distribution by reversed-phase high-pressure liquid chromatography revealed slightly decreased peptide cross-linking and an increased average glycan chain length compared to those of the parent. These results together suggest that a transglycosylase activity was enhanced in the mutant. This may represent a novel mechanism of glycopeptide resistance in S. aureus.

Intermediate filaments: molecular architecture, assembly, dynamics and polymorphism

1999 ◽  
Vol 32 (2) ◽  
pp. 99-187 ◽  
Author(s):  
David A. D. Parry ◽  
Peter M. Steinert
Keyword(s):  
Intermediate Filaments ◽  
Intermediate Filament ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Lattice Structure ◽  
Coiled Coil ◽  
Salt Bridges ◽  
Molecular Architecture

1. Introduction 1002. Molecular architecture 1072.1 Primary structure 1082.1.1 Homologous regions 1092.1.2 Chain typing 1152.1.3 Post-translational modifications 1172.2 Secondary structure 1182.2.1 Central rod domain 1182.2.2 Head and tail domains 1192.3 Tertiary structure 1232.3.1 Coiled-coil rod domain 1232.3.1.1 Specificity through salt bridges 1242.3.1.2 Specificity through apolar interactions 1272.3.1.3 A consensus trigger sequence for two-stranded coiled-coils 1282.3.2 Discontinuities in the rod domain 1282.3.2.1 Links 1292.3.2.2 Stutter 1312.3.3 Head and tail domains 1312.4 Electron microscope observations 1333. Assembly 1363.1 Role of the coiled-coil rod domain 1373.2 Role of end domains 1413.3 Experimentally induced crosslinks and modes of assembly 1453.4 Naturally occurring crosslinks for tissue coordination 1543.5 STEM data 1544. Quaternary structure 1604.1 Protofilaments and protofibrils 1604.2 Head and tail domains 1634.3 Surface lattice structure 1644.4 Crystal studies on intermediate filament fragments 1685. Polymorphism 1695.1 Variations on a theme 1705.1.1 Axial structure 1705.1.2 Lateral structure 1716. Keratin intermediate filament chains in diseases 1727. Concluding remarks 1758. Acknowledgments 1769. References 176Three types of intracellular filament have been identified in eukaryotic cells, and together they constitute the key elements of the cytoskeleton. They are the microtubules, the actin-containing microfilaments and the intermediate filaments. The uniqueness of the former two types of filament in cells has been well known for a long time but, in contrast, the intermediate filaments have been a relative new-comer to the scene. The microtubules and the microfilaments have always been easy to distinguish from one another on the grounds of their respective sizes (microtubules are about 25 nm in diameter and microfilaments are about 7–10 nm in diameter). Additionally, microtubules were capable of being disaggregated by the action of colchicine, and microfilaments could be disassembled by other drugs or be decorated with heavy meromyosin to generate arrowhead-like structures. Importantly, in both microtubules and microfilaments the constituent protein subunits were arranged to give the filaments a directionality, and the ability of these filaments to function in vivo depended crucially on this feature of their structure. Microtubules, for example, are involved in mitosis, motility and transport within the cell: each of these functions is clearly a ‘directional’ one. With this background the discovery and characterization of the intermediate filaments can begin.

scholarly journals Tertiary Structure of Staphylococcus aureus Cell Wall Murein

2004 ◽  
Vol 186 (21) ◽  
pp. 7141-7148 ◽  
Author(s):  
Boris A. Dmitriev ◽  
Filip V. Toukach ◽  
O. Holst ◽  
E. T. Rietschel ◽  
S. Ehlers
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Plasma Membrane ◽  
Tertiary Structure ◽  
Gram Positive ◽  
Division Plane ◽  
Gram Positive Bacteria ◽  
Computer Simulation Studies ◽  
High Degree ◽  
Division Plane Orientation

ABSTRACT The recently described scaffold model of murein architecture depicts the gram-negative bacterial cell wall as a gel-like matrix composed of cross-linked glycan strands oriented perpendicularly to the plasma membrane while peptide bridges adopt a parallel orientation (B. A. Dmitriev, F. V. Toukach, K. J. Schaper, O. Holst, E. T. Rietschel, and S. Ehlers, J. Bacteriol. 185:3458-3468, 2003). Based on the scaffold model, we now present computer simulation studies on the peptidoglycan arrangement of the gram-positive organism Staphylococcus aureus, which show that the orientation of peptide bridges is critical for the highly cross-linked murein architecture of this microorganism. According to the proposed refined model, staphylococcal murein is composed of glycan and oligopeptide chains, both running in a plane that is perpendicular to the plasma membrane, with oligopeptide chains adopting a zigzag conformation and zippering adjacent glycan strands along their lengths. In contrast to previous models of murein in gram-positive bacteria, this model reflects the high degree of cross-linking that is the hallmark of the staphylococcal cell wall and is compatible with distinguishing features of S. aureus cytokinesis such as the triple consecutive alteration of the division plane orientation and the strictly centripetal mode of septum closure.

scholarly journals Predicting division planes of three-dimensional cells by soap-film minimization

2017 ◽  
Author(s):  
Pablo Martinez ◽  
Lindy A. Allsman ◽  
Kenneth A. Brakke ◽  
Christopher Hoyt ◽  
Jordan Hayes ◽  
...  
Keyword(s):  
Developmental Regulation ◽  
Three Dimensional ◽  
Soap Film ◽  
Preprophase Band ◽  
Animal Cells ◽  
Division Plane ◽  
Plane Orientation ◽  
Division Site ◽  
Division Plane Orientation

AbstractOne key aspect of cell division in multicellular organisms is the orientation of the division plane. Proper division plane establishment contributes to normal organization of the plant body. To determine the importance of cell geometry in division plane orientation, we designed a threedimensional probabilistic mathematical modeling approach to directly test the century-old hypothesis that cell divisions mimic “soap-film minima” or that daughter cells have equal volume and the resulting division plane is a local surface area minimum. Predicted division planes were compared to a plant microtubule array that marks the division site, the preprophase band (PPB). PPB location typically matched one of the predicted divisions. Predicted divisions offset from the PPB occurred when a neighboring cell wall or PPB was observed directly adjacent to the predicted division site, to avoid creating a potentially structurally unfavorable four-way junction. By comparing divisions of differently shaped plant and animal cells to divisions simulated in silico, we demonstrate the generality of this model to accurately predict in vivo division. This powerful model can be used to separate the contribution of geometry from mechanical stresses or developmental regulation in predicting division plane orientation.

Substructure of crystalline peroxisomes in methanol-grown Hansenula polymorpha: evidence for an in vivo crystal of alcohol oxidase

1981 ◽  
Vol 1 (10) ◽  
pp. 949-957
Author(s):  
M Veenhuis ◽  
W Harder ◽  
J P van Dijken ◽  
F Mayer
Keyword(s):  
Osmotic Shock ◽  
Hansenula Polymorpha ◽  
Three Dimensional ◽  
Alcohol Oxidase ◽  
Molecular Architecture ◽  
Three Dimensional Model ◽  
Structural Element ◽  
Free Mobility ◽  
Crystalline Matrix

The substructural organization of completely crystalline peroxisomes present in Hansenula polymorpha cells grown under methanol limitation in a chemostat was investigated by different cytochemical and ultrastructural techniques. Time-dependent cytochemical staining experiments indicated that activities of the two main constituents of these organelles, namely, alcohol oxidase and catalase, were present throughout the crystalline matrix. Catalase was completely removed from isolated peroxisomes by osmotic shock treatment. After such treatment, the ultrastructure of the crystalline matrix of the organelles remained virtually intact. Because alcohol oxidase activity was still present in this matrix, it was concluded that alcohol oxidase protein is the only structural element of the peroxisomal crystalloids. The molecular architecture of the crystalloids was investigated in ultrathin cryosections which permitted recognition of individual molecules in the crystalline matrix. Depending on the plane of sectioning, different crystalline patterns were observed. Tilting experiments indicated that these images were caused by superposition of octameric alcohol oxidase molecules arranged in a tetragonal lattice. A three-dimensional model of the crystalloid is presented. The repeating unit of this structure is composed of four alcohol oxidase molecules. The crystalloid represents an open structure, which may explain the observed free mobility of catalase molecules.

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