How electrostatic networks modulate specificity and stability of collagen

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

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Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile

10.21203/rs.3.rs-1018941/v1 ◽

2021 ◽

Author(s):

Akihiro Kawamoto ◽

Tomohito Yamada ◽

Toru Yoshida ◽

Takayuki Kato ◽

Hideaki Tsuge

Keyword(s):

High Resolution ◽

Structural Information ◽

Host Cells ◽

Binary Toxin ◽

Specific Interactions ◽

Clostridioides Difficile ◽

Toxin Complex ◽

High Resolution Structure ◽

Partial Unfolding ◽

Resolution Structure

Abstract Besides two large cytotoxins (TcdA and TcdB), certain Clostridioides difficile strains also produce a binary toxin, called C. difficile toxin (CDT) composed of an enzymatic subunit involved in actin ADP-ribosylation (CDTa) and translocation pore (CDTb) that delivers CDTa into host cells through receptor-mediated endocytosis. CDTb is proposed to be a di-heptamer, but its physiological heptameric structure has not been reported to date. Here, we report the CDTa-bound CDTb-pore (heptamer) as a physiological complexes using cryo-EM. The high-resolution structure of the CDTa-bound CDTb-pore at 2.56-Å resolution revealed that CDTa binding to CDTb-pore induces partial unfolding and tilting of the first CDTa a-helix, and the translocation. In the CDTb-pore, the NSS-loop exists in “in” and “out” conformations, suggesting their involvement in substrate translocation through formation of weak, non-specific interactions. This structural information provides insights into drug design against hypervirulent C. difficile strains.

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Electron Diffraction of Platinum Labelled Bacteriorhodopsin

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s143192760000012x ◽

1980 ◽

Vol 38 ◽

pp. 34-35

Author(s):

M. E. Dumont ◽

J. W. Wiggins ◽

S. B. Hayward

Keyword(s):

Amino Acids ◽

High Resolution ◽

Electron Diffraction ◽

Structural Information ◽

Heavy Atom ◽

Halobacterium Halobium ◽

Heavy Atoms ◽

Isomorphous Replacement ◽

Atom Localization ◽

Resolution Structure

We are using electron diffraction to characterize a platinum-containing derivative of bacteriorhodopsin, the light-driven proton pump from Halobacterium halobium. This has been undertaken with the dual aims of: 1)using the method of multiple heavy atom isomorphous replacement to obtain high resolution structural information about the protein, and 2)locating heavy atom labelled amino acids in the structure in order to correlate the recently determined sequence with the structural map. A necessary first step in such studies is the location of the heavy atoms in the low resolution structure. This report focusses on ways of dealing with the inherent statistical uncertainties encountered in this heavy atom localization.

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Fibril formation through self-assembly of a simple glycine derivative and X-ray diffraction study

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1515/zkri-2019-0062 ◽

2020 ◽

Vol 235 (1-2) ◽

pp. 47-51

Author(s):

Arpita Dutta ◽

Suven Das ◽

Purak Das ◽

Suvendu Maity ◽

Prasanta Ghosh

Keyword(s):

Hydrogen Bonding ◽

Solid State ◽

High Resolution ◽

Diffraction Study ◽

Self Assembly ◽

Van Der Waals Interactions ◽

Base Catalyst ◽

X Ray Diffraction ◽

X Ray ◽

Sheet Structure

AbstractN-(N-benzoyl glycinyl)-N,N′-dicyclohexylurea was synthesised by conjugating N-benzoyl glycine and dicyclohexylcarbodiimide (DCC) using triethylamine as base catalyst. A single crystal X-ray diffraction study reveals that the compound self-assembles into a supramolecular sheet structure by intermolecular N–H · · · O, C–H · · · O hydrogen bonding and non-bonding van der Waals interactions. A high resolution transmission electronic microscopic (HR-TEM) image of the compound exhibits formation of fibrils in the solid state.

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High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble β-Sheet Scaffold

Journal of Molecular Biology ◽

10.1016/j.jmb.2008.02.051 ◽

2008 ◽

Vol 378 (2) ◽

pp. 459-467 ◽

Cited By ~ 12

Author(s):

Koki Makabe ◽

Matthew Biancalana ◽

Shude Yan ◽

Valentina Tereshko ◽

Grzegorz Gawlak ◽

...

Keyword(s):

High Resolution ◽

Self Assembly ◽

Hydrophobic Peptide ◽

High Resolution Structure ◽

Β Sheet ◽

Resolution Structure

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High-resolution crystal structures of two crystal forms of human cyclophilin D in complex with PEG 400 molecules

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14009480 ◽

2014 ◽

Vol 70 (6) ◽

pp. 717-722 ◽

Cited By ~ 3

Author(s):

Koteswara Rao Valasani ◽

Emily A. Carlson ◽

Kevin P. Battaile ◽

Andrea Bisson ◽

Chunyu Wang ◽

...

Keyword(s):

High Resolution ◽

Crystal Structures ◽

Structural Information ◽

Amyloid Β ◽

Crystal Form ◽

Cyclophilin D ◽

Crystal Forms ◽

Peg 400 ◽

Mitochondrial Target ◽

Resolution Structure

Cyclophilin D (CypD) is a key mitochondrial target for amyloid-β-induced mitochondrial and synaptic dysfunction and is considered a potential drug target for Alzheimer's disease. The high-resolution crystal structures of primitive orthorhombic (CypD-o) and primitive tetragonal (CypD-t) forms have been determined to 1.45 and 0.85 Å resolution, respectively, and are nearly identical structurally. Although an isomorphous structure of CypD-t has previously been reported, the structure reported here was determined at atomic resolution, while CypD-o represents a new crystal form for this protein. In addition, each crystal form contains a PEG 400 molecule bound to the same region along with a second PEG 400 site in CypD-t which occupies the cyclosporine A inhibitor binding site of CypD. Highly precise structural information for CypD should be extremely useful for discerning the detailed interaction of small molecules, particularly drugs and/or inhibitors, bound to CypD. The 0.85 Å resolution structure of CypD-t is the highest to date for any CypD structure.

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High-Resolution Scanning Electron Microscopy of Biological Specimens

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100103012 ◽

1988 ◽

Vol 46 ◽

pp. 186-187

Author(s):

M. Müller ◽

R. Hermann

Keyword(s):

High Resolution ◽

Freeze Drying ◽

Room Temperature ◽

Structural Information ◽

Freeze Substitution ◽

Critical Point Drying ◽

Sem Study ◽

Major Factors ◽

Structural Preservation ◽

Preparation Techniques

Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.

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Progress in high-resolution CRYO-SEM imaging of viral particles

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100166555 ◽

1996 ◽

Vol 54 ◽

pp. 818-819

Author(s):

Ya Chen ◽

Geoffrey Letchworth ◽

John White

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

High Resolution ◽

Structural Information ◽

Signal To Noise Ratio ◽

Flexible Structures ◽

Simian Virus ◽

Topographic Features ◽

Viral Particles ◽

Scanning Electron

Low-temperature high-resolution scanning electron microscopy (cryo-HRSEM) has been successfully utilized to image biological macromolecular complexes at nanometer resolution. Recently, imaging of individual viral particles such as reovirus using cryo-HRSEM or simian virus (SIV) using HRSEM, HV-STEM and AFM have been reported. Although conventional electron microscopy (e.g., negative staining, replica, embedding and section), or cryo-TEM technique are widely used in studying of the architectures of viral particles, scanning electron microscopy presents two major advantages. First, secondary electron signal of SEM represents mostly surface topographic features. The topographic details of a biological assembly can be viewed directly and will not be obscured by signals from the opposite surface or from internal structures. Second, SEM may produce high contrast and signal-to-noise ratio images. As a result of this important feature, it is capable of visualizing not only individual virus particles, but also asymmetric or flexible structures. The 2-3 nm resolution obtained using high resolution cryo-SEM made it possible to provide useful surface structural information of macromolecule complexes within cells and tissues. In this study, cryo-HRSEM is utilized to visualize the distribution of glycoproteins of a herpesvirus.

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Atomic chemistry by HREM and image simulations?

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100145480 ◽

1986 ◽

Vol 44 ◽

pp. 828-829

Author(s):

J.M. Howe ◽

R. Gronsky

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Structural Information ◽

High Resolution Electron Microscopy ◽

Resolution Electron ◽

Image Simulations

The technique of high-resolution electron microscopy (HREM) is invaluable to the materials scientist because it allows examination of microstructural features at levels of resolution that are unobtainable by most other methods. Although the structural information which can be determined by HREM and accompanying image simulations has been well documented in the literature, there have only been a few cases where this technique has been used to reveal the chemistry of individual columns or planes of atoms, as occur in segregated and ordered materials.

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