scholarly journals Structural anatomy of C1 domain interactions with DAG and other agonists

2021 ◽  
Author(s):  
Sachin S Katti ◽  
Inna V Krieger ◽  
Jihyae Ann ◽  
Jeewoo Lee ◽  
James C Sacchettini ◽  
...  
Keyword(s):  
High Resolution ◽  
Structural Information ◽  
Biological Membrane ◽  
Lipid Binding ◽  
Effector Proteins ◽  
Downstream Signaling ◽  
Cellular Processes ◽  
C1 Domain ◽  
Domain Interactions ◽  
C1 Domains

Diacylglycerol (DAG) is a versatile lipid whose 1,2-sn-stereoisomer serves both as second messenger in signal transduction pathways that control vital cellular processes, and as metabolic precursor for downstream signaling lipids such as phosphatidic acid. DAG effector proteins compete for available lipid using conserved homology 1 (C1) domains as DAG-sensing modules. Yet, how C1 domains recognize and capture DAG in the complex environment of a biological membrane has remained unresolved for the 40 years since the discovery of Protein Kinase C (PKC) as the first member of the DAG effector cohort. Herein, we report the first high-resolution crystal structures of a C1 domain (C1B from PKCdelta) complexed to DAG and to each of four potent PKC agonists that produce different biological readouts and that command intense therapeutic interest. This structural information details the mechanisms of stereospecific recognition of DAG by the C1 domains, the functional properties of the lipid-binding site, and the identities of the key residues required for the recognition and capture of DAG and exogenous agonists. Moreover, the structures of the five C1 domain complexes provide the high-resolution guides for the design of agents that modulate the activities of DAG effector proteins.

scholarly journals p23/Tmp21 Differentially Targets the Rac-GAP β2-Chimaerin and Protein Kinase C via Their C1 Domains

2010 ◽  
Vol 21 (8) ◽  
pp. 1398-1408 ◽  
Author(s):  
HongBin Wang ◽  
Marcelo G. Kazanietz
Keyword(s):  
Protein Kinase C ◽  
Protein Kinase ◽  
Protein Interactions ◽  
Phorbol Esters ◽  
Lipid Binding ◽  
Kinase C ◽  
C1 Domain ◽  
Pkc Isozymes ◽  
Domain Docking ◽  
C1 Domains

The C1 domains in protein kinase C (PKC) isozymes and other signaling molecules are responsible for binding the lipid second messenger diacylglycerol and phorbol esters, and for mediating translocation to membranes. Previous studies revealed that the C1 domain in α- and β-chimaerins, diacylglycerol-regulated Rac-GAPs, interacts with the endoplasmic reticulum/Golgi protein p23/Tmp21. Here, we found that p23/Tmp21 acts as a C1 domain-docking protein that mediates perinuclear translocation of β2-chimaerin. Glu227 and Leu248 in the β2-chimaerin C1 domain are crucial for binding p23/Tmp21 and perinuclear targeting. Interestingly, isolated C1 domains from individual PKC isozymes differentially interact with p23/Tmp21. For PKCε, it interacts with p23/Tmp21 specifically via its C1b domain; however, this association is lost in response to phorbol esters. These results demonstrate that p23/Tmp21 acts as an anchor that distinctively modulates compartmentalization of C1 domain-containing proteins, and it plays an essential role in β2-chimaerin relocalization. Our study also highlights the relevance of C1 domains in protein–protein interactions in addition to their well-established lipid-binding properties.

High-Resolution Scanning Electron Microscopy of Biological Specimens

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.

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

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.

Atomic chemistry by HREM and image simulations?

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.

Pushing the Envelope

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Structural Information ◽  
Hydration Shell ◽  
Three Dimensional ◽  
Scattering Data ◽  
Saxs Data ◽  
Electron Density Function ◽  
Angle Scattering ◽  
Iterative Structure

Direct electron density determination from SAXS data opens up new opportunities. The ability to model density at high resolution and the implicit direct estimation of solvent terms such as the hydration shell may enable high-resolution wide angle scattering data to be used to calculate density when combined with additional structural information. Other diffraction methods that do not measure three-dimensional intensities, such as fiber diffraction, may also be able to take advantage of iterative structure factor retrieval. While the ability to reconstruct electron density ab initio is a major breakthrough in the field of solution scattering, the potential of the technique has yet to be fully uncovered. Additional structural information from techniques such as crystallography, NMR, and electron microscopy and density modification procedures can now be integrated to perform advanced modeling of the electron density function at high resolution, pushing the boundaries of solution scattering further than ever before.

Characterization of Tilt Boundaries by Ultra High Resolution Electron Microscopy

1984 ◽  
Vol 41 ◽  
Author(s):  
W. Krakow ◽  
J. T. Wetzel ◽  
D. A. Smith ◽  
G. Trafas
Keyword(s):  
High Resolution ◽  
Grain Boundary ◽  
Structural Information ◽  
Theoretical Work ◽  
High Resolution Electron Microscopy ◽  
Point Of View ◽  
Experimental Point ◽  
Structure Information ◽  
Resolution Electron ◽  
Tilt Boundaries

AbstractA high resolution electron microscope study of grain boundary structures in Au thin films has been undertaken from both a theoretical and experimental point of view. The criteria necessary to interpret images of tilt boundaries at the atomic level, which include electron optical and specimen effects, have been considered for both 200kV and the newer 400kV medium voltage microscopes. So far, the theoretical work has concentrated on two different [001] tilt bounda-ries where a resolution of 2.03Å is required to visualize bulk lattice structures on either side of the interface. Both a high angle boundary, (210) σ=5, and a low angle boundary, (910) σ=41, have been considered. Computational results using multislice dynamical diffraction and image simulations of relaxed bounda-ries viewed edge-on and with small amounts of beam and/or specimen inclina-tion have been obtained. It will be shown that some structural information concerning grain boundary dislocations can be observed at 200kV. However, many difficulties occur in the exact identification of the interface structure viewed experimentally for both [001] and [011] boundaries since the resolution required is near the performance limit of a 200kV microscope. The simulated results at 400kV indicate a considerable improvement will be realized in obtain-ing atomic structure information at the interface.

scholarly journals Measurement of synchrotron-radiation-excited Kossel patterns

2016 ◽  
Vol 23 (1) ◽  
pp. 214-218 ◽  
Author(s):  
G. Bortel ◽  
G. Faigel ◽  
M. Tegze ◽  
A. Chumakov
Keyword(s):  
High Resolution ◽  
Dynamic Range ◽  
Structural Information ◽  
Photon Counting ◽  
Spot Size ◽  
Low Noise ◽  
X Rays ◽  
Technical Problems ◽  
Pixel Detectors ◽  
Exciting Beam

Kossel line patterns contain information on the crystalline structure, such as the magnitude and the phase of Bragg reflections. For technical reasons, most of these patterns are obtained using electron beam excitation, which leads to surface sensitivity that limits the spatial extent of the structural information. To obtain the atomic structure in bulk volumes, X-rays should be used as the excitation radiation. However, there are technical problems, such as the need for high resolution, low noise, large dynamic range, photon counting, two-dimensional pixel detectors and the small spot size of the exciting beam, which have prevented the widespread use of Kossel pattern analysis. Here, an experimental setup is described, which can be used for the measurement of Kossel patterns in a reasonable time and with high resolution to recover structural information.

Three-Dimensional High Resolution Scaffold Fiber Architecture and Morphology in Tissue Engineered Heart Valve Tissue

2010 ◽  
Author(s):  
Chad E. Eckert ◽  
Brandon T. Mikulis ◽  
Dane Gerneke ◽  
Danielle Gottlieb ◽  
Bruce Smaill ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
High Resolution ◽  
Heart Valve ◽  
Structural Information ◽  
Three Dimensional ◽  
Tissue Scaffold ◽  
Valve Tissue ◽  
Sampling Protocols ◽  
Heart Valve Tissue

Engineered heart valve tissue (EHVT) has received much attention as a potential pediatric valve replacement therapy, offering prospective long-term functional improvements over current options. A significant gap in the literature exists, however, regarding estimating tissue mechanical properties from tissue-scaffold composites. Detailed three-dimensional structural information prior to implantation (in vitro) and after implantation in (in vivo) is needed for improved modeling of tissue properties. As such, a novel high-resolution imaging technique will be employed to obtain three-dimensional microstructural information. Analysis techniques will be used to fully quantify constituents of interest including scaffold, collagen, and cellular information and to develop appropriate two-dimensional sectioning sampling protocols. It is the intent of this work to guide modeling efforts to better elucidate EHVT tissue-specific mechanical properties.

scholarly journals High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form

2018 ◽  
Vol 74 (11) ◽  
pp. 717-724 ◽  
Author(s):  
Shukun Luo ◽  
Ke Xu ◽  
Shaoyun Xiang ◽  
Jie Chen ◽  
Chunyun Chen ◽  
...  
Keyword(s):  
Drug Discovery ◽  
High Resolution ◽  
Crystal Structures ◽  
Active Site ◽  
Crystal Form ◽  
Crystal Forms ◽  
Cellular Processes ◽  
Potential Target ◽  
Indoleamine 2,3 Dioxygenase

Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2–2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å resolution and can be readily used for soaking experiments to determine high-resolution structures of IDO1 in complex with the substrate tryptophan or inhibitors that coordinate the heme. In addition, this mutant was used to produce crystals of a complex with an inhibitor that targets the apo form of the enzyme under the same conditions; the structure of this complex was determined at 1.7 Å resolution. Overall, this mutant represents a robust platform for determining the structures of inhibitor and substrate complexes of IDO1 at high resolution.

scholarly journals Allostery revealed within lipid binding events to membrane proteins

2018 ◽  
Vol 115 (12) ◽  
pp. 2976-2981 ◽  
Author(s):  
John W. Patrick ◽  
Christopher D. Boone ◽  
Wen Liu ◽  
Gloria M. Conover ◽  
Yang Liu ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Protein Interactions ◽  
Biological Membrane ◽  
Binding Constants ◽  
Native Mass Spectrometry ◽  
Specific Protein ◽  
Lipid Binding ◽  
Allosteric Modulation ◽  
Lipid Species ◽  
Specific Lipid

Membrane proteins interact with a myriad of lipid species in the biological membrane, leading to a bewildering number of possible protein−lipid assemblies. Despite this inherent complexity, the identification of specific protein−lipid interactions and the crucial role of lipids in the folding, structure, and function of membrane proteins is emerging from an increasing number of reports. Fundamental questions remain, however, regarding the ability of specific lipid binding events to membrane proteins to alter remote binding sites for lipids of a different type, a property referred to as allostery [Monod J, Wyman J, Changeux JP (1965)J Mol Biol12:88–118]. Here, we use native mass spectrometry to determine the allosteric nature of heterogeneous lipid binding events to membrane proteins. We monitored individual lipid binding events to the ammonia channel (AmtB) fromEscherichia coli, enabling determination of their equilibrium binding constants. We found that different lipid pairs display a range of allosteric modulation. In particular, the binding of phosphatidylethanolamine and cardiolipin-like molecules to AmtB exhibited the largest degree of allosteric modulation, inspiring us to determine the cocrystal structure of AmtB in this lipid environment. The 2.45-Å resolution structure reveals a cardiolipin-like molecule bound to each subunit of the trimeric complex. Mutation of a single residue in AmtB abolishes the positive allosteric modulation observed for binding phosphatidylethanolamine and cardiolipin-like molecules. Our results demonstrate that specific lipid−protein interactions can act as allosteric modulators for the binding of different lipid types to integral membrane proteins.

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