scholarly journals Molecular mechanism of light-driven sodium pumping

2020 ◽  
Author(s):  
K. Kovalev ◽  
R. Astashkin ◽  
I. Gushchin ◽  
P. Orekhov ◽  
D. Volkov ◽  
...  
Keyword(s):  
High Resolution ◽  
Molecular Mechanism ◽  
Close Relation ◽  
Proton Pumps ◽  
Ion Release ◽  
Sodium Pumps ◽  
Functional Studies ◽  
Ion Translocation ◽  
Cation Pump ◽  
New Discovery

ABSTRACTMicrobial rhodopsins appeared to be the most abundant light-harvesting proteins on the Earth and are the major contributes to the solar energy captured in the sea. They possess highly diverse biological functions. Explosion of research on microbial rhodopsins led to breakthroughs in their applications, in particular, in neuroscience.An unexpected new discovery was a Na+-pumping KR2 rhodopsin from Krokinobacter eikastus, the first light-driven non-proton cation pump. A fundamental difference between proton and other cation pumps is that non-proton pumps cannot use tunneling or Grotthuss mechanism for the ion translocation and, therefore, Na+ pumping cannot be understood in the framework of classical proton pump, like bacteriorhodopsin. Extensive studies on the molecular mechanism of KR2 failed to reveal mechanism of pumping. The existing high-resolution structures relate only to the ground state of the protein and revealed no Na+ inside the protein, which is unusual for active ion transporters.KR2 is only known non proton cation transporter with demonstrated remarkable potential for optogenetic applications and, therefore, elucidation of the mechanism of cation transport is important. To understand conception of cation pumping we solved crystal structures of the functionally key O-intermediate state of physiologically relevant pentameric form of KR2 and its D116N and H30A key mutants at high resolution and performed additional functional studies.The structure of the O-state reveals a sodium ion near the retinal Schiff base coordinated by N112 and D116 residues of the characteristic (for the whole family) NDQ triad. The structural and functional data show that cation uptake and release are driven by a switching mechanism. Surprisely, Na+ pathway in KR2 is lined with the chain of polar pores/cavities, similarly to the channelrhodopsin-2. Using Parinello fast molecular dynamics approach we obtained a molecular movie of a probable ion release.Our data provides insight into the mechanism of a non-proton cation light-driven pumping, strongly suggest close relation of sodium pumps to channel rhodopsins and, we believe, expand the present knowledge of rhodopsin world. Certainly they might be used for engineering of cation pumps and ion channels for optogenetics.

scholarly journals A Roadmap for Intestinal Regeneration

2020 ◽  
Vol 52 ◽  
Author(s):  
David Quispe-Parra ◽  
Griselle Valentín ◽  
José E. García-Arrarás
Keyword(s):  
Molecular Mechanism ◽  
Sea Cucumber ◽  
Regenerative Process ◽  
Research Model ◽  
Functional Studies ◽  
Cellular Processes ◽  
Sequencing Technologies ◽  
Cellular Events ◽  
Intestinal Regeneration ◽  
Holothuria Glaberrima

Regeneration of lost or injured organs is an intriguing process where numerous cellular events take place to form the new structure. Studies of this process during reconstitution of the intestine have been performed in echinoderms, particularly in holothurians. Many cellular events triggered during regeneration have been described using the sea cucumber Holothuria glaberrima as a research model. More recent experiments have targeted the molecular mechanism behind the process, a task that has been eased by the new sequencing technologies now available. In this review we present the studies involving cellular processes and the genes that have been identified to be associated with the early events of gut regeneration. We also present the ongoing efforts to perform functional studies necessary to establish the role(s) of the identified genes. A synopsis of the studies is given with the course of the regenerative process established so far.

Coverage Effects and the Nature of the Metal−Sulfur Bond in S/Au(111):  High-Resolution Photoemission and Density-Functional Studies

2003 ◽  
Vol 125 (1) ◽  
pp. 276-285 ◽  
Author(s):  
José A. Rodriguez ◽  
Joseph Dvorak ◽  
Tomas Jirsak ◽  
Gang Liu ◽  
Jan Hrbek ◽  
...  
Keyword(s):  
High Resolution ◽  
Density Functional ◽  
Functional Studies ◽  
Coverage Effects ◽  
Sulfur Bond

STEP SIZE IN ACTIVATED RABBIT SARCOMERES IS INDEPENDENT OF FILAMENT OVERLAP

2004 ◽  
Vol 04 (04) ◽  
pp. 485-498 ◽  
Author(s):  
EKATERINA M. NAGORNYAK ◽  
GERALD H. POLLACK ◽  
FELIX A. BLYAKHMAN
Keyword(s):  
Molecular Structure ◽  
High Resolution ◽  
Molecular Mechanism ◽  
Thin Filament ◽  
Sarcomere Length ◽  
Psoas Muscle ◽  
Length Change ◽  
Step Size ◽  
Resolution Algorithm ◽  
Parallel Measurements

Investigations carried out on single cardiac and bumblebee myofibrils have shown stepwise sarcomere-length change of ~2.7 nm.1 We have carried out parallel measurements on single myofibrils from rabbit psoas muscle. Activated specimens were released or stretched using a motor-imposed ramp. With a high-resolution algorithm, we found that step sizes were always integer multiples of 2.7 nm, whether the length change was positive or negative, and independent of ramp velocity. Also, the influence of initial sarcomere length was studied, and found to be negligible. The value 2.7 nm, seen consistently, is equal to the linear repeat of actin monomers along the thin filament, a result that ties dynamical events to molecular structure, and places narrow constraints on any proposed molecular mechanism.

scholarly journals High-resolution regulatory maps connect cardiovascular risk variants to disease related pathways

2018 ◽  
Author(s):  
Örjan Åkerborg ◽  
Rapolas Spalinskas ◽  
Sailendra Pradhananga ◽  
Anandashankar Anil ◽  
Pontus Höjer ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
High Resolution ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Cvd Risk ◽  
Expression Levels ◽  
Functional Studies ◽  
Multiple Promoters ◽  
Risk Variants ◽  
Coding Variants

AbstractGenetic variant landscape of cardiovascular disease (CVD) is dominated by non-coding variants among which many occur within putative enhancers regulating the expression levels of relevant genes. It is crucial to assign the genetic variants to their correct gene both to gain insights into perturbed functions and better assess the risk of disease. In this study, we generated high-resolution genomic interaction maps (~750 bases) in aortic endothelial, smooth muscle and THP-1 macrophages using Hi-C coupled with sequence capture targeting 25,429 features including variants associated with CVD. We detected interactions for 761 CVD risk variants obtained by genome-wide association studies (GWAS) and identified novel as well as established functions associated with CVD. We were able to fine-map 331 GWAS variants using interaction networks, thereby identifying additional genes and functions. We also discovered a subset of risk variants interacting with multiple promoters and the expression levels of such genes were correlated. The presented resource enables functional studies of cardiovascular disease providing novel approaches for its diagnosis and treatment.

scholarly journals Structural basis of nanobody-recognition of grapevine fanleaf virus and of virus resistance loss

2019 ◽  
Author(s):  
Igor Orlov ◽  
Caroline Hemmer ◽  
Léa Ackerer ◽  
Bernard Lorber ◽  
Ahmed Ghannam ◽  
...  
Keyword(s):  
High Resolution ◽  
Binding Site ◽  
Molecular Mechanism ◽  
Virus Resistance ◽  
Plant Virus ◽  
Structural Basis ◽  
Grapevine Fanleaf Virus ◽  
Induced Fit ◽  
Resistance Breaking ◽  
Resistance Loss

AbstractGrapevine fanleaf virus (GFLV) is a picorna-like plant virus transmitted by nematodes that affects vineyards worldwide. Nanobody (Nb)-mediated resistance against GFLV has been created recently and shown to be highly effective in plants including grapevine, but the underlying mechanism is unknown. Here we present the high-resolution cryo-EM structure of the GFLV-Nb23 complex which provides the basis for the molecular recognition by the nanobody. The structure reveals a composite binding site bridging over 3 domains of the capsid protein (CP) monomer. The structure provides a precise mapping of the Nb23 epitope on the GFLV capsid in which the antigen loop is accommodated through an induced fit mechanism. Moreover, we uncover and characterize several resistance-breaking GFLV isolates with amino acids mapping within this epitope, including C-terminal extensions of the CP, which would sterically interfere with Nb binding. Escape variants with such extended CP fail to be transmitted by nematodes linking Nb-mediated resistance to vector transmission. Together, these data provide insights into the molecular mechanism of Nb23-mediated recognition of GFLV and of virus resistance loss.SignificanceGrapevine fanleaf virus (GFLV) is a picorna-like plant virus that severely impacts vineyards worldwide. While Nanobodies (Nb) confer resistance to GFLV in plants the underlying molecular mechanism of action is unknown. Here we present the high-resolution cryo-EM structure of the GFLV-Nb complex. It uncovers the conformational epitope on the capsid surface which is a composite binding site into which the antigen loop is accommodated through an induced fit mechanism. Furthermore, we describe several resistance-breaking isolates of GFLV with reduced Nb binding capacity. Those that carry a C-terminal extension also fail to be transmitted by nematodes. Together, these data provide structure-function insights into the Nb-GFLV recognition and the molecular mechanism leading to loss of resistance.

scholarly journals Structure of the RZZ complex and molecular basis of Spindly-driven corona assembly at human kinetochores

2021 ◽  
Author(s):  
Tobias Raisch ◽  
Giuseppe Ciossani ◽  
Ennio d’Amico ◽  
Verena Cmentowski ◽  
Sara Carmignani ◽  
...  
Keyword(s):  
High Resolution ◽  
Binding Site ◽  
Molecular Mechanism ◽  
Building Block ◽  
Molecular Basis ◽  
Spindle Assembly Checkpoint ◽  
Spindle Assembly ◽  
Structural Requirements ◽  
Necessary And Sufficient

In metazoans, a ≍1 megadalton (MDa) super-complex comprising the Dynein-Dynactin adaptor Spindly and the ROD-Zwilch-ZW10 (RZZ) complex is the building block of a fibrous biopolymer, the kinetochore fibrous corona. The corona assembles on mitotic kinetochores to promote microtubule capture and spindle assembly checkpoint (SAC) signaling. We report here a high-resolution cryo-EM structure that captures the essential features of the RZZ complex, including a farnesyl binding site required for Spindly binding. Using a highly predictive in vitro assay, we demonstrate that the SAC kinase MPS1 is necessary and sufficient for corona assembly at supercritical concentrations of the RZZ-Spindly (RZZS) complex, and describe the molecular mechanism of phosphorylation-dependent filament nucleation. We identify several structural requirements for RZZS polymerization in rings and sheets. Finally, we identify determinants of kinetochore localization and corona assembly of Spindly. Our results describe a framework for the long-sought-for molecular basis of corona assembly on metazoan kinetochores.

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