Structure and Action of Molecular Tracks and Motors

1998 ◽  
Vol 4 (S2) ◽  
pp. 456-457
Author(s):  
R.A. Milligan
Keyword(s):  
Conformational Changes ◽  
Molecular Motors ◽  
Three Dimensional ◽  
X Ray ◽  
Myosin I ◽  
Structure Determinations ◽  
Moderate Resolution ◽  
Mechanochemical Cycle ◽  
The Individual ◽  
Muscle Myosin

Molecular motors belonging to the myosin and kinesin superfamilies utilize ATP to move along their respective F-actin and microtubule tracks. The track-motor complexes have not been amenable to crystallization, so x-ray crystallographic investigations have focused on structure determinations of the individual proteins. Although providing detailed descriptions of the structure of each protein, this approach cannot reveal the geometry of interaction of the proteins nor the conformational changes which occur during the mechanochemical cycle. To obtain this information, we use cryoelectron microscopy and image analysis to calculate three dimensional maps of the track-motor complexes at moderate resolution (15-30A) and combine these data with the high resolution x-ray structures to provide near-atomic models of the working assemblies.We have so far built models of the rigor (nucleotide-free) and ADP actomyosin complexes. In smooth muscle myosin II (a collaboration with H.L. Sweeney, U. Perm.) and brush border myosin I (BBMI), the motor domain of the myosin head is similar in both biochemical states.

Numerical study of the second harmonic generation in FELs

2021 ◽  
Vol 28 (3) ◽  
Author(s):  
A. M. Kalitenko
Keyword(s):  
Second Harmonic Generation ◽  
Harmonic Generation ◽  
Free Electron ◽  
Numerical Study ◽  
Second Harmonic ◽  
Three Dimensional ◽  
X Ray ◽  
Linac Coherent Light Source ◽  
The Individual ◽  
Analytical Expressions

A numerical study of the effect of betatron oscillations on the second harmonic generation in free-electron lasers (FELs) is presented. Analytical expressions for the effective coupling strength factors are derived that clearly distinguish all contributions in subharmonics and each polarization of the radiation. A three-dimensional time-dependent numerical FEL code that takes into account the main FEL effects and the individual contribution of each electron to the second harmonic generation is presented. Also, the X- and Y-polarizations of the second harmonic are analyzed. The second harmonic was detected in experiments at the Advanced Photon Source (APS) Low Energy Undulator Test Line (LEUTL) and Linac Coherent Light Source (LCLS) in the soft X-ray regime. The approach presented in the article can be useful for a comprehensive study and diagnostics of XFELs. In the paper, the LCLS and Pohang Accelerator Laboratory X-ray Free-Electron Laser (PAL-XFEL) experiments are modeled. The simulation results are in a good agreement with the experimental data.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

Structural Systematics of 2/4-Nitrophenoxide Complexes of Closed-Shell Metal Ions. VII Acid Salts of the 4-Nitrophenoxides of Group 2

1998 ◽  
Vol 51 (8) ◽  
pp. 785 ◽  
Author(s):  
Jack M. Harrowfield ◽  
Raj Pal Sharma ◽  
Brian W. Skelton ◽  
Allan H. White
Keyword(s):  
Room Temperature ◽  
Calcium Salt ◽  
Three Dimensional ◽  
Closed Shell ◽  
The Other ◽  
X Ray ◽  
C 23 ◽  
Structure Determinations ◽  
Group 2 ◽  
Acid Salts

Room-temperature single-crystal X-ray structure determinations are recorded for a number of Group 2 4-nitrophenoxide acid salts, variously hydrated M(4-np)2.x(4-npH).yH2O. Ca(4-np)2.2(4-npH).8H2O is monoclinic, P 21/n, a 30·52(1), b 10·027(1), c 23·65(2) Å, β 116·3(5)°, Z = 8, conventional R on |F| being 0·058 for No 5092 independent ‘observed’ (I > 3s(I)) reflections. Sr(4-np)2.2(4-npH).8H2O, based on a subcell of the former, is monoclinic, P 21/c, a 15·576(5), b10·081(6), c 24·20(2) Å, β 117·99(5)° , Z = 4, R 0·054 for No 2908. Ba(4-np)2.2(4-npH).4H2O is orthorhombic, Fdd2, a 28·01(1), b 19·90(1), c 10·692(7)Å, Z = 8, R 0·028 for No 1967. The strontium array (and that of the calcium salt developed from it) may be represented as [(H2O)6Sr(4-npH.4-np)] (4-npH.4-np), a neutral ligand being unsymmetrically chelated to the strontium through the nitro group, with a quasi-parallel counter ion hydrogen-bonded to it by phenoxide confrontation. The other two 4-np residues make up a similar phenoxide-confronting pair (4-npH.4-np), the hydrogen being more intimately associated with one moiety. The barium salt is also an interesting array: the 10-coordinate barium lies on a crystallographic 2 axis, in an environment of two pairs of symmetry-related nitro-chelating ligand anions, and a pair of nitro-O coordinating neutral 4-npH ligands; the whole [(H2O)4Ba(4-np)2(4-npH)2] array may be envisaged as a single neutral (super)molecule. Hydrogen bonds between confronting phenoxides of the neutral 4-npH components of the parent and the 4-np- components of neighbouring molecules link the whole into a three-dimensional array.

Donor-Akzeptor-Komplexe von Halogenidionen mit 1.4-Diiodtetrafluorbenzol/Donor-Acceptor Complexes of Halide Ions with 1,4-Diiodotetrafluorobenzene

1999 ◽  
Vol 54 (1) ◽  
pp. 77-86 ◽  
Author(s):  
Jutta Grebe ◽  
Gertraud Geiseler ◽  
Klaus Harms ◽  
Kurt Dehnicke
Keyword(s):  
Three Dimensional ◽  
Crystallographic Structure ◽  
Acceptor Molecule ◽  
Halide Ions ◽  
Space Group ◽  
X Ray ◽  
Bond Angles ◽  
Structure Determinations ◽  
Donor Acceptor

(Ph4P)X as well as (Me4N)X (X = Cl, Br, I) react with 1,4-diiodotetrafluorobenzene in CH2C12 and CH3CN solutions, respectively, to give the donoracceptor complexes (Ph4PM (C6F4I2)Cl2]·4 CH2Cl2 (1), (Ph4P)2[(C6F4I2)Br2]·2 CH2Cl2 (2), (Me4N)[(C6F4I2)Cl] (3), (Me4N)[(C6F4I2)Br]·CH3CN (4), (Ph4P)2[(C6F4I2)3Br2]·4CH2Cl2 (5), (Ph4P)2[(C6F4I2)3I2] (6) and (Me4N)2[(C6F4I2)3I2] (7). All complexes have been characterized by single X-ray crystallographic structure determinations. 1: Space group P1̄, Z = 1, lattice dimensions at 203 K: a = 1090.2(1), b = 1206.2(1), c = 1242.8(1) pm, α = 91,84(1)°, β = 106.60(1)°, γ = 99.84(1)°.2: Space group P1̄, Z = 1, lattice dimensions at 233 K: a = 1129.7(2), b = 1183.9(1), c = 1293.4(1) pm, α = 65.52(1)°, β = 65.74(1)°, γ = 89.02(1)°.3: Space group P21/n, Z = 4, lattice dimensions at 243 K: a = 714.8(1), b = 2405.7(3), c = 930.8(1) pm, β = 96.38(1)°.4: Space group P21/c, Z = 4, lattice dimensions at 203 K: a = 1400.8(1), b = 1669.9(2), c = 795.9(1) pm, β = 102.81(1)°.5: Space group Pbca, Z = 4, lattice dimensions at 223 K: a = 2106.0(4), b = 1566.8(3), c = 2445.8(4) pm.6 : Space group P1̄, Z = 1, lattice dimensions at 203 K: a = 1150.9(1), b = 1278.9(1), c = 1292.9(2) pm, α = 65.47(1)°, β = 82.07(1)°, γ = 83.62(1)°.7: Space group Pbca, Z = 4, lattice dimensions at 223 K: a = 1210.5(5), b = 1429.0(6), c = 2470.3(12) pm.In all complexes the acceptor molecule C6F4I2 coordinates with the halide donor ions in linear arrangements C-I· · ·X- . In 1 and 2 the halide ions act as terminal donors to form the dianionic species [X· · ·I-C6F4-I· · ·X]2- (X = Cl, Br). Complexes 3 and 4 form polymeric anionic zigzag chains with μ-X- bridges and bond angles I· · ·Cl· · ·I of 77.2° and I· · ·Br· · ·I of 74.3°. Complexes 5 - 7 are characterized by three-dimensional anionic networks via /x3-X- bridging halide ions and μ-bridging 1,4-diiodotetrafluorobenzene molecules.

scholarly journals RasC Plays a Role in Transduction of Temporal Gradient Information in the Cyclic-AMP Wave of Dictyostelium discoideum

2004 ◽  
Vol 3 (3) ◽  
pp. 646-662 ◽  
Author(s):  
Deborah Wessels ◽  
Rebecca Brincks ◽  
Spencer Kuhl ◽  
Vesna Stepanovic ◽  
Karla J. Daniels ◽  
...  
Keyword(s):  
Cyclic Amp ◽  
Myosin Ii ◽  
Three Dimensional ◽  
Computer Assisted ◽  
Expression Array ◽  
Temporal Gradient ◽  
Spatial Gradients ◽  
Quantitative Studies ◽  
Myosin I ◽  
The Individual

ABSTRACT To define the role that RasC plays in motility and chemotaxis, the behavior of a rasC null mutant, rasC −, in buffer and in response to the individual spatial, temporal, and concentration components of a natural cyclic AMP (cAMP) wave was analyzed by using computer-assisted two-dimensional and three-dimensional motion analysis systems. These quantitative studies revealed that rasC − cells translocate at the same velocity and exhibit chemotaxis up spatial gradients of cAMP with the same efficiency as control cells. However, rasC − cells exhibit defects in maintaining anterior-posterior polarity along the substratum and a single anterior pseudopod when translocating in buffer in the absence of an attractant. rasC − cells also exhibit defects in their responses to both the increasing and decreasing temporal gradients of cAMP in the front and the back of a wave. These defects result in the inability of rasC − cells to exhibit chemotaxis in a natural wave of cAMP. The inability to respond normally to temporal gradients of cAMP results in defects in the organization of the cytoskeleton, most notably in the failure of both F actin and myosin II to exit the cortex in response to the decreasing temporal gradient of cAMP in the back of the wave. While the behavioral defect in the front of the wave is similar to that of the myoA −/myoF − myosin I double mutant, the behavioral and cytoskeletal defects in the back of the wave are similar to those of the S13A myosin II regulatory light-chain phosphorylation mutant. Expression array data support the premise that the behavioral defects exhibited by the rasC − mutant are the immediate result of the absence of RasC function.

Dimensional Quantification of Embedded Voids or Objects in Three Dimensions Using X-Ray Tomography

2012 ◽  
Vol 18 (2) ◽  
pp. 390-398 ◽  
Author(s):  
Brian M. Patterson ◽  
Juan P. Escobedo-Diaz ◽  
Darcie Dennis-Koller ◽  
Ellen Cerreta
Keyword(s):  
Digital Imaging ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Post Processing ◽  
X Ray ◽  
Individual Object ◽  
Starting Point ◽  
X Ray Computed ◽  
The Individual ◽  
Processing Steps

AbstractScientific digital imaging in three dimensions such as when using X-ray computed tomography offers a variety of ways to obtain, filter, and quantify data that can produce vastly different results. These opportunities, performed during image acquisition or during the data processing, can include filtering, cropping, and setting thresholds. Quantifying features in these images can be greatly affected by how the above operations are performed. For example, during binarization, setting the threshold too low or too high can change the number of objects as well as their measured diameter. Here, two facets of three-dimensional quantification are explored. The first will focus on investigating the question of how many voxels are needed within an object to have accurate geometric statistics that are due to the properties of the object and not an artifact of too few voxels. These statistics include but are not limited to percent of total volume, volume of the individual object, Feret shape, and surface area. Using simple cylinders as a starting point, various techniques for smoothing, filtering, and other processing steps can be investigated to aid in determining if they are appropriate for a specific desired statistic for a real dataset. The second area of investigation is the influence of post-processing, particularly segmentation, on measuring the damage statistics in high purity Cu. The most important parts of the pathways of processing are highlighted.

scholarly journals Insights into the mechanisms of myosin and kinesin molecular motors from the single-molecule unbinding force measurements

2010 ◽  
Vol 7 (suppl_3) ◽  
Author(s):  
Sergey V. Mikhailenko ◽  
Yusuke Oguchi ◽  
Shin'ichi Ishiwata
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Force Measurements ◽  
Cellular Functions ◽  
Mechanochemical Cycle ◽  
The Individual ◽  
Experimental Geometry ◽  
External Loads ◽  
Individual Motor

In cells, ATP (adenosine triphosphate)-driven motor proteins, both cytoskeletal and nucleic acid-based, operate on their corresponding ‘tracks’, that is, actin, microtubules or nucleic acids, by converting the chemical energy of ATP hydrolysis into mechanical work. During each mechanochemical cycle, a motor proceeds via several nucleotide states, characterized by different affinities for the ‘track’ filament and different nucleotide (ATP or ADP) binding kinetics, which is crucial for a motor to efficiently perform its cellular functions. The measurements of the rupture force between the motor and the track by applying external loads to the individual motor–substrate bonds in various nucleotide states have proved to be an important tool to obtain valuable insights into the mechanism of the motors' performance. We review the application of this technique to various linear molecular motors, both processive and non-processive, giving special attention to the importance of the experimental geometry.

scholarly journals Three-dimensional visualisation of the internal anatomy of the sparrowhawk (Accipiter nisus) forelimb using contrast-enhanced micro-computed tomography

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3039 ◽  
Author(s):  
Fernanda Bribiesca-Contreras ◽  
William I. Sellers
Keyword(s):  
Computed Tomography ◽  
3D Model ◽  
Three Dimensional ◽  
Biomechanical Analysis ◽  
X Ray ◽  
Accipiter Nisus ◽  
Contrast Enhanced ◽  
Muscle Geometry ◽  
The Individual ◽  
Non Destructive

BackgroundGross dissection is a widespread method for studying animal anatomy, despite being highly destructive and time-consuming. X-ray computed tomography (CT) has been shown to be a non-destructive alternative for studying anatomical structures. However, in the past it has been limited to only being able to visualise mineralised tissues. In recent years, morphologists have started to use traditional X-ray contrast agents to allow the visualisation of soft tissue elements in the CT context. The aim of this project is to assess the ability of contrast-enhanced micro-CT (μCT) to construct a three-dimensional (3D) model of the musculoskeletal system of the bird wing and to quantify muscle geometry and any systematic changes due to shrinkage. We expect that this reconstruction can be used as an anatomical guide to the sparrowhawk wing musculature and form the basis of further biomechanical analysis of flight.MethodsA 3% iodine-buffered formalin solution with a 25-day staining period was used to visualise the wing myology of the sparrowhawk (Accipiter nisus). μCT scans of the wing were taken over the staining period until full penetration of the forelimb musculature by iodine was reached. A 3D model was reconstructed by manually segmenting out the individual elements of the avian wing using 3D visualisation software.ResultsDifferent patterns of contrast were observed over the duration of the staining treatment with the best results occurring after 25 days of staining. Staining made it possible to visualise and identify different elements of the soft tissue of the wing. Finally, a 3D reconstruction of the musculoskeletal system of the sparrowhawk wing is presented and numerical data of muscle geometry is compared to values obtained by dissection.DiscussionContrast-enhanced μCT allows the visualisation and identification of the wing myology of birds, including the smaller muscles in the hand, and provides a non-destructive way for quantifying muscle volume with an accuracy of 96.2%. By combining contrast-enhanced μCT with 3D visualisation techniques, it is possible to study the individual muscles of the forelimb in their original position and 3D design, which can be the basis of further biomechanical analysis. Because the stain can be washed out post analysis, this technique provides a means of obtaining quantitative muscle data from museum specimens non-destructively.

X-Ray Structure Determinations of Bromo- and/or Bromomethylsubstituted Benzenes: C–H···Br, C–Br···Br, and C–Br···π Interactions

2012 ◽  
Vol 67 (12) ◽  
pp. 1273-1281 ◽  
Author(s):  
Peter G. Jones ◽  
Piotr Kuś ◽  
Ina Dix
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Benzene Derivatives ◽  
Chemical Similarity ◽  
X Ray ◽  
Π Interactions ◽  
Layer Structures ◽  
Structure Determinations ◽  
Subordinate Role

The structures of seven benzene derivatives [1,2,3-tri(bromomethyl)benzene, (1); 3,5- di(bromomethyl)bromobenzene, (2); 2,5-di(bromomethyl)bromobenzene, (3); 4-(bromomethyl)-2,5- dibromotoluene, (4); 4-(bromomethyl)bromobenzene, (5); 2,3-di(bromomethyl)bromobenzene, (6) and (bromomethyl)-p-dibromobenzene, (7)] with bromo and bromomethyl (and in one case methyl) substituents are presented and analysed in terms of Br···Br interactions up to 4.0 A° , supported by hydrogen bonds H···Br. Some interactions of the type Br···π and π···π are encountered and play a subordinate role in the packing. Despite the close chemical similarity of the compounds, some of which are isomers with permuted substituent positions, the packing motifs are highly variable. Compounds 2-5 are based on layer structures with Brn (n=3, 4) and/or mixed Br/C rings. Compounds 1, 6 and 7 display three-dimensional packings of differing complexity, but with interpretable substructures; 1 can be analysed in terms of ribbons of linked Br3 and Br4 rings; 6 displays chains of linked Br3 triangles; 7 consists of ribbons of linked Br4 quadrilaterals.

New aspects of the nitration of some imidazo[1,2-a]pyridines. CNDO/2 calculations from X-ray structures

1982 ◽  
Vol 35 (9) ◽  
pp. 1761 ◽  
Author(s):  
JC Teulade ◽  
R Escale ◽  
JC Rossi ◽  
JP Chapat ◽  
G Grassy ◽  
...  
Keyword(s):  
Experimental Results ◽  
X Ray ◽  
Structure Determinations ◽  
The Individual ◽  
System 1

The reactivity of the imidazo[l,2-a]pyridine system (1) was investigated, CNDO/2 calculations based on X-ray structure determinations of 5-ethoxyimidazo[l,2-a]pyridine (2), ethyl 8-methylimidazo-[1,2-a]pyridine-2-carboxylate (5) and ethyl 6-methyl-3-nitroimidazo[l,2-a]pyridine-2-carboxylate (10c) are compared with experimental results of the nitration of variously substituted imidazo[l,2-a]- pyridines, and are found compatible with the individual reactivities.

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