Key role of excess atomic volume in structural rearrangements at the front of moving partial dislocations in copper nanocrystals

The Frank–Starling mechanism of the heart is due, in part, to modulation of myofilament Ca2+ sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WT muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank–Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA.

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The role of structural imperfections in the photodimerization of 9-cyanoanthracene

Proceedings of the Royal Society of London Series A - Mathematical and Physical Sciences ◽

10.1098/rspa.1971.0150 ◽

1971 ◽

Vol 324 (1559) ◽

pp. 459-468 ◽

Cited By ~ 43

Keyword(s):

Fluorescence Microscopy ◽

Excitation Energy ◽

Slip Plane ◽

Stacking Faults ◽

Stacking Fault ◽

Burgers Vector ◽

Partial Dislocations ◽

Structural Imperfections ◽

Active Slip

Crystalline 9-cyanoanthracene undergoes photodimerization to give the trans dimer which is unexpected on the basis of the topochemical preformation theory. The possibility that the reaction occurs at defects is investigated; and the nature of the structural imperfections are described, as are also the types of product nuclei and their modes of growth. Interference-contrast and fluorescence microscopy have been employed for the examination of cleaved and partially dimerized faces of the monomer. It is shown that there is an active slip plane (221), and consideration of feasible dislocation reactions, particularly those involving unit strength dislocations which have a component of the Burgers vector in [100], reveals that, within stacking-fault regions (bounded by partial dislocations), the monomer molecules are in trans registry. It is suggested that molecules in such stacking faults act as traps for the excitation energy, and that reaction occurs at these sites.

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Modelling the Activation Pathways in Full-Length Src Kinase

Biophysica ◽

10.3390/biophysica1020018 ◽

2021 ◽

Vol 1 (2) ◽

pp. 238-248

Author(s):

Josephine Alba ◽

Maria Montagna ◽

Marco D’Abramo

Keyword(s):

Experimental Data ◽

Structural Rearrangements ◽

Dynamic Simulations ◽

Src Inhibitor ◽

Molecular Determinants ◽

Complex Protein ◽

Depth Study ◽

Cell Processes ◽

Activation Pathways

Src kinases play fundamental roles in several crucial cell processes. Their activity is tightly regulated by conformational transitions between the active and the inactive forms, which are carried out by complex protein structural rearrangements. Here, we present an in-depth study of such structural transitions coupling extensive all-atoms molecular dynamic simulations coupled to an algorithm able to drive the system between defined conformational states. Our results, in line with the available experimental data, confirm the complexity of such a process indicating the main molecular determinants involved. Moreover, the role of an Src inhibitor—able to bind to the protein inactive state—is discussed and compared with available experimental data.

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The possible role of partial dislocations in facilitating transformations of the Nishiyama–Wassermann type

Scripta Materialia ◽

10.1016/j.scriptamat.2004.09.031 ◽

2005 ◽

Vol 52 (3) ◽

pp. 175-179 ◽

Cited By ~ 18

Author(s):

John J. Jonas ◽

Youliang He ◽

Stéphane Godet

Keyword(s):

Partial Dislocations

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Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome

10.1101/841262 ◽

2019 ◽

Author(s):

Evan J. Worden ◽

Xiangbin Zhang ◽

Cynthia Wolberger

Keyword(s):

Histone Methylation ◽

Structural Basis ◽

Structural Rearrangements ◽

H3k4 Methylation ◽

Core Complex ◽

Histone H2b ◽

Protein Core ◽

The Face ◽

Histone H3k4

ABSTRACTMethylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation.

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Nucleation of γ' plates from G.P. zones in an Al-Ag alloy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100144231 ◽

1986 ◽

Vol 44 ◽

pp. 552-553

Author(s):

J.M. Howe ◽

R. Gronsky

Keyword(s):

Alternative View ◽

Ion Milling ◽

Frank Loop ◽

Shockley Partial ◽

Partial Dislocations ◽

Thin Foils ◽

Nucleation Sites ◽

Equilibrium Phases ◽

Experimental And Theoretical Studies

Experimental and theoretical studies on the role of G.P. zones in the nucleation of either transition or equilibrium phases have been an active area of research for many years. In Al-Ag alloys, these zones are not usually thought to serve as nucleation sites for metastable γ' plates, although the alternative view was expressed during early research on this system. Instead, γ' plates are nucleated either by the splitting of perfect a/2<110> dislocations into pairs of a/6<112> Shockley partial dislocations, or by the propagation of a Shockley partial dislocation across an a/3<111> Frank loop. The stacking faults produced by these reactions thus create an initial two-atom layer of hep γ' precipitate. However, in this study it was found that γ' plates can nucleate from G.P. zones during ion milling of thin foils prior to TEM examination.

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Role of Pseudouridine in Structural Rearrangements of Helix 69 During Bacterial Ribosome Assembly

ACS Chemical Biology ◽

10.1021/cb200497q ◽

2012 ◽

Vol 7 (5) ◽

pp. 871-878 ◽

Cited By ~ 16

Author(s):

Yogo Sakakibara ◽

Christine S. Chow

Keyword(s):

Ribosome Assembly ◽

Structural Rearrangements ◽

Helix 69 ◽

Bacterial Ribosome

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The Yield Stress Anomaly in Fe-Al Alloys: The Role of the Local Climb Locking Mechanism

MRS Proceedings ◽

10.1557/proc-364-79 ◽

1994 ◽

Vol 364 ◽

Cited By ~ 3

Author(s):

David G. Morris ◽

David Peguiron

Keyword(s):

Yield Stress ◽

Detailed Examination ◽

Al Alloys ◽

Al Alloy ◽

Al Content ◽

Partial Dislocations ◽

Locking Mechanism ◽

Crystallographic Axes ◽

Ordered State

AbstractA detailed examination of the variation of yield stress with temperature in an Fe3Al alloy shows a maximum at a temperature of about 500°C, slightly below the critical temperature for loss of DO3 order. At this temperature the dislocations present in the material change from being <111= superdislocations separated by APB to being single dislocations with Burgers vector <100=. At slightly lower temperatures the superdislocations become pinned by a local climb process involving point defect transfer between the partial dislocations.Analysis of the forces between the dislocations which induce the local climb locking process allows an estimation of the role which will be played by variations in composition of the Fe-Al alloy considered, changes in deformation rate and orientation of the applied stress.Examination of data available in the literature shows that each of the three aspects discussed, namely the influence of variations in ordered state, in Al content over the range 25% to 50%, or additions of alloying elements such as Si, straining at very fast or at slow rates, and stressing along different crystallographic axes, is completely consistent with the model proposed.

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Crystal structure of an archaeal CorB magnesium transporter

Nature Communications ◽

10.1038/s41467-021-24282-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yu Seby Chen ◽

Guennadi Kozlov ◽

Brandon E. Moeller ◽

Ahmed Rohaim ◽

Rayan Fakih ◽

...

Keyword(s):

Crystal Structure ◽

Analytical Ultracentrifugation ◽

Structural Rearrangements ◽

Exchange Mass Spectrometry ◽

Magnesium Transporter ◽

Hydrogen Deuterium ◽

Deuterium Exchange Mass Spectrometry ◽

Atp Sensing

AbstractCNNM/CorB proteins are a broadly conserved family of integral membrane proteins with close to 90,000 protein sequences known. They are associated with Mg2+ transport but it is not known if they mediate transport themselves or regulate other transporters. Here, we determine the crystal structure of an archaeal CorB protein in two conformations (apo and Mg2+-ATP bound). The transmembrane DUF21 domain exists in an inward-facing conformation with a Mg2+ ion coordinated by a conserved π-helix. In the absence of Mg2+-ATP, the CBS-pair domain adopts an elongated dimeric configuration with previously unobserved domain-domain contacts. Hydrogen-deuterium exchange mass spectrometry, analytical ultracentrifugation, and molecular dynamics experiments support a role of the structural rearrangements in mediating Mg2+-ATP sensing. Lastly, we use an in vitro, liposome-based assay to demonstrate direct Mg2+ transport by CorB proteins. These structural and functional insights provide a framework for understanding function of CNNMs in Mg2+ transport and associated diseases.

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