scholarly journals Signaling Networks and Dynamics of Allosteric Transitions in Bacterial Chaperonin GroEL: Implications for Iterative Annealing of Misfolded Proteins

2017 ◽  
Author(s):  
D. Thirumalai ◽  
Changbong Hyeon
Keyword(s):  
Signal Transmission ◽  
Signaling Networks ◽  
Salt Bridges ◽  
Wiring Diagram ◽  
Chaperonin Groel ◽  
Consistent Manner ◽  
Allosteric Transitions ◽  
Biological Complexes ◽  
And Function ◽  
Molecular Description

AbstractSignal transmission at the molecular level in many biological complexes occurs through allosteric transitions. They describe the response a complex to binding of ligands at sites that are spatially well separated from the binding region. We describe the Structural Perturbation Method (SPM), based on phonon propagation in solids, that can be used to determine the signal transmitting allostery wiring diagram (AWD) in large but finite-sized biological complexes. Applications to the bacterial chaperonin GroEL-GroES complex shows that the AWD determined from structures also drive the allosteric transitions dynamically. Both from a structural and dynamical perspective these transitions are largely determined by formation and rupture of salt-bridges. The molecular description of allostery in GroEL provides insights into its function, which is quantitatively described by the Iterative Annealing Mechanism. Remarkably, in this complex molecular machine, a deep connection is established between the structures, reaction cycle during which GroEL undergoes a sequence of allosteric transitions, and function in a self-consistent manner.

scholarly journals Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins

2018 ◽  
Vol 373 (1749) ◽  
pp. 20170182 ◽  
Author(s):  
D. Thirumalai ◽  
Changbong Hyeon
Keyword(s):  
Molecular Level ◽  
Signal Transmission ◽  
Salt Bridges ◽  
Wiring Diagram ◽  
Chaperonin Groel ◽  
Consistent Manner ◽  
Allosteric Transitions ◽  
Biological Complexes ◽  
And Function ◽  
Molecular Description

Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. Allostery describes the responses of a complex to binding of ligands at sites that are spatially well separated from the binding region. We describe the structural perturbation method, based on phonon propagation in solids, which can be used to determine the signal-transmitting allostery wiring diagram (AWD) in large but finite-sized biological complexes. Application to the bacterial chaperonin GroEL–GroES complex shows that the AWD determined from structures also drives the allosteric transitions dynamically. From both a structural and dynamical perspective these transitions are largely determined by formation and rupture of salt-bridges. The molecular description of allostery in GroEL provides insights into its function, which is quantitatively described by the iterative annealing mechanism. Remarkably, in this complex molecular machine, a deep connection is established between the structures, reaction cycle during which GroEL undergoes a sequence of allosteric transitions, and function, in a self-consistent manner. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.

scholarly journals Stoichiometry and Turnover of the Bacterial Flagellar Switch Protein FliN

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Nicolas J. Delalez ◽  
Richard M. Berry ◽  
Judith P. Armitage
Keyword(s):  
Copy Number ◽  
Motor Proteins ◽  
Fluorescent Protein ◽  
Protein Complexes ◽  
Content Type ◽  
Rotation Direction ◽  
Cell Measurement ◽  
Biological Complexes ◽  
And Function

ABSTRACTSome proteins in biological complexes exchange with pools of free proteins while the complex is functioning. Evidence is emerging that protein exchange can be part of an adaptive mechanism. The bacterial flagellar motor is one of the most complex biological machines and is an ideal model system to study protein dynamics in large multimeric complexes. Recent studies showed that the copy number of FliM in the switch complex and the fraction of FliM that exchanges vary with the direction of flagellar rotation. Here, we investigated the stoichiometry and turnover of another switch complex component, FliN, labeled with the fluorescent protein CyPet, inEscherichia coli. Our results confirm that,in vivo, FliM and FliN form a complex with stoichiometry of 1:4 and function as a unit. We estimated that wild-type motors contained 120 ± 26 FliN molecules. Motors that rotated only clockwise (CW) or counterclockwise (CCW) contained 114 ± 17 and 144 ± 26 FliN molecules, respectively. The ratio of CCW-to-CW FliN copy numbers was 1.26, very close to that of 1.29 reported previously for FliM. We also measured the exchange of FliN molecules, which had a time scale and dependence upon rotation direction similar to those of FliM, consistent with an exchange of FliM-FliN as a unit. Our work confirms the highly dynamic nature of multimeric protein complexes and indicates that, under physiological conditions, these machines might not be the stable, complete structures suggested by averaged fixed methodologies but, rather, incomplete rings that can respond and adapt to changing environments.IMPORTANCEThe flagellum is one of the most complex structures in a bacterial cell, with the core motor proteins conserved across species. Evidence is now emerging that turnover of some of these motor proteins depends on motor activity, suggesting that turnover is important for function. The switch complex transmits the chemosensory signal to the rotor, and we show, by using single-cell measurement, that both the copy number and the fraction of exchanging molecules vary with the rotational bias of the rotor. When the motor is locked in counterclockwise rotation, the copy number is similar to that determined by averaged, fixed methodologies, but when locked in a clockwise direction, the number is much lower, suggesting that that the switch complex ring is incomplete. Our results suggest that motor remodeling is an important component in tuning responses and adaptation at the motor.

scholarly journals TORC2-Gad8-dependent myosin phosphorylation modulates regulation by calcium

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Karen Baker ◽  
Irene A Gyamfi ◽  
Gregory I Mashanov ◽  
Justin E Molloy ◽  
Michael A Geeves ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Growth ◽  
Cell Cycle Progression ◽  
Actin Polymerization ◽  
Neck Region ◽  
Signaling Networks ◽  
Tor Signaling ◽  
Multicellular Development ◽  
Membrane Reorganization ◽  
And Function

Cells respond to changes in their environment through signaling networks that modulate cytoskeleton and membrane organization to coordinate cell-cycle progression, polarized cell growth and multicellular development. Here, we define a novel regulatory mechanism by which the motor activity and function of the fission yeast type one myosin, Myo1, is modulated by TORC2-signalling-dependent phosphorylation. Phosphorylation of the conserved serine at position 742 (S742) within the neck region changes both the conformation of the neck region and the interactions between Myo1 and its associating calmodulin light chains. S742 phosphorylation thereby couples the calcium and TOR signaling networks that are involved in the modulation of myosin-1 dynamics to co-ordinate actin polymerization and membrane reorganization at sites of endocytosis and polarised cell growth in response to environmental and cell-cycle cues.

scholarly journals Form and Function Predict Acoustic Transmission Properties of the Songs of Male and Female Canyon Wrens

2021 ◽  
Vol 9 ◽  
Author(s):  
Lauryn Benedict ◽  
Braelei Hardt ◽  
Lorraine Dargis
Keyword(s):  
Signal Transmission ◽  
Male And Female ◽  
Male Song ◽  
Form And Function ◽  
Transmission Properties ◽  
Use Context ◽  
Males And Females ◽  
Song Transmission ◽  
Typical Habitat ◽  
And Function

To function effectively, animal signals must transmit through the environment to receivers, and signal transmission properties depend on signal form. Here we investigated how the transmission of multiple parts of a well-studied signal, bird song, varies between males and females of one species. We hypothesized that male and female songs would have different transmission properties, reflecting known differences in song form and function. We further hypothesized that two parts of male song used differentially in broadcast singing and aggressive contests would transmit differently. Analyses included male and female songs from 20 pairs of canyon wrens (Catherpes mexicanus) played and re-recorded in species-typical habitat. We found that male song cascades used in broadcast singing propagated farther than female songs, with higher signal-to-noise ratios at distance. In contrast, we demonstrated relatively restricted propagation of the two vocalization types typically used in short-distance aggressive signaling, female songs and male “cheet” notes. Of the three tested signals, male “cheet” notes had the shortest modeled propagation distances. Male and female signals blurred similarly, with variable patterns of excess attenuation. Both male song parts showed more consistent transmission across the duration of the signal than did female songs. Song transmission, thus, varied by sex and reflected signal form and use context. Results support the idea that males and females of the same species can show distinctly different signal evolution trajectories. Sexual and social selection pressures can shape sex-specific signal transmission, even when males and females are communicating in shared physical environments.

scholarly journals Transmembrane signaling and cytoplasmic signal conversion by dimeric transmembrane helix 2 and a linker domain of the DcuS sensor kinase

2020 ◽  
pp. jbc.RA120.015999
Author(s):  
Marius Stopp ◽  
Philipp Aloysius Steinmetz ◽  
Christopher Schubert ◽  
Christian Griesinger ◽  
Dirk Schneider ◽  
...  
Keyword(s):  
Signal Transmission ◽  
Transmembrane Helix ◽  
Helical Structure ◽  
Kinase Domain ◽  
Sensor Kinase ◽  
Transmembrane Signaling ◽  
Activated State ◽  
Sensor Kinases ◽  
And Function ◽  
Cytoplasmic Side

Transmembrane signaling is a key process of membrane bound sensor kinases. The C4-dicarboxylate (fumarate) responsive sensor kinase DcuS of Escherichia coli is anchored by transmembrane helices TM1 and TM2 in the membrane. Signal transmission across the membrane relies on the piston-type movement of the periplasmic part of TM2. To define the role of TM2 in transmembrane signaling, we use oxidative Cys cross-linking to demonstrate that TM2 extends over the full distance of the membrane and forms a stable transmembrane homodimer in both the inactive and fumarate-activated state of DcuS. A S186xxxGxxxG194 motif is required for the stability and function of the TM2 homodimer. The TM2 helix further extends on the periplasmic side into the α6-helix of the sensory PASP domain, and on the cytoplasmic side into the α1-helix of PASC. PASC has to transmit the signal to the C-terminal kinase domain. A helical linker on the cytoplasmic side connecting TM2 with PASC contains a LxxxLxxxL sequence. The dimeric state of the linker was relieved during fumarate activation of DcuS, indicating structural rearrangements in the linker. Thus, DcuS contains a long α-helical structure reaching from the sensory PASP (α6) domain across the membrane to α1(PASC). Taken together, the results suggest piston-type transmembrane signaling by the TM2-homodimer from PASP across the full TM region, whereas the fumarate-destabilized linker dimer converts the signal on the cytoplasmic side for PASC and kinase regulation.

scholarly journals Refinement of a Cryo-EM Structure of hERG: Bridging Structure and Function

2020 ◽  
Author(s):  
H.M. Khan ◽  
J. Guo ◽  
H.J. Duff ◽  
D. P. Tieleman ◽  
S. Y. Noskov
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Salt Bridge ◽  
Structure And Function ◽  
Channel Structure ◽  
Salt Bridges ◽  
Voltage Sensing ◽  
Chain Conformations ◽  
And Function ◽  
Voltage Sensing Domain

AbstractThe human ether-a-go-go-related gene (hERG) encodes the voltage gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using Molecular Dynamics Flexible Fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG.Statement of SignificanceCryo-EM has emerged as a major breakthrough technique in structural biology of membrane proteins. However, even high-resolution Cryo-EM structures contain poor side chain conformations and interatomic clashes. A high-resolution cryo-EM structure of hERG1 has been solved in the depolarized (open) state. The state captured by Cryo-EM surprisingly did not feature many functionally important interactions established by previous experiments. Molecular Dynamics Flexible Fitting (MDFF) used to enable refinement of the hERG1 channel structure in complex membrane environment re-establishing key functional interactions in the voltage sensing domain.

scholarly journals Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses

2021 ◽  
Author(s):  
Rouven Schulz ◽  
Medina Korkut-Demirbaş ◽  
Gloria Colombo ◽  
Sandra Siegert
Keyword(s):  
Signaling Pathways ◽  
Protein Interactions ◽  
Immune Cell ◽  
Signal Transmission ◽  
The Body ◽  
Cell Type ◽  
Protein Protein Interactions ◽  
Β2 Adrenergic Receptor ◽  
Neuronal Signal ◽  
And Function

G protein-coupled receptors (GPCRs) regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell type-specific responses when the same GPCR is expressed on different cells within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest. We show that the chimeric DREADD-β2-adrenergic receptor (β2AR/ADRB2) triggers comparable responses to levalbuterol on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in microglia, a β2AR-expressing immune cell that can drive inflammation in the nervous system. To further dissect microglial inflammation, we compared DREADD-β2AR with two additionally designed DREADD-based chimeras mimicking GPR65 and GPR109A/HCAR2, both enriched in microglia. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A had no impact. Our DREADD-based approach allows investigation of cell type-dependent signaling pathways and function without known endogenous ligands.

scholarly journals Targeting Raf Kinase Inhibitory Protein Regulation and Function

Cancers ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 306 ◽  
Author(s):  
Ali Yesilkanal ◽  
Marsha Rosner
Keyword(s):  
Tumor Cells ◽  
Molecular Mechanisms ◽  
Kinase Inhibitor ◽  
Signaling Networks ◽  
Metastasis Suppressor ◽  
Metastatic Progression ◽  
Inhibitory Protein ◽  
Raf Kinase ◽  
Raf Kinase Inhibitory Protein ◽  
And Function

Raf Kinase Inhibitory Protein (RKIP) is a highly conserved kinase inhibitor that functions as a metastasis suppressor in a variety of cancers. Since RKIP can reprogram tumor cells to a non-metastatic state by rewiring kinase networks, elucidating the mechanism by which RKIP acts not only reveals molecular mechanisms that regulate metastasis, but also represents an opportunity to target these signaling networks therapeutically. Although RKIP is often lost during metastatic progression, the mechanism by which this occurs in tumor cells is complex and not well understood. In this review, we summarize our current understanding of RKIP regulation in tumors and consider experimental and computational strategies for recovering or mimicking its function by targeting mediators of metastasis.

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