scholarly journals Structure of transmembrane helix 8 and possible membrane defects in CFTR

2017 ◽  
Author(s):  
Valentina Corradi ◽  
Ruo-Xu Gu ◽  
Paola Vergani ◽  
D. Peter Tieleman
Keyword(s):  
Cystic Fibrosis ◽  
Abc Transporter ◽  
Bound States ◽  
Transmembrane Helix ◽  
Md Simulations ◽  
Atp Binding ◽  
Gating Mechanism ◽  
Membrane Defects ◽  
Dynamics Simulations ◽  
Atp Binding And Hydrolysis

ABSTRACTThe cystic fibrosis transmembrane conductance regulator (CFTR) is an ion channel that regulates the flow of anions across epithelia. Mutations in CFTR cause cystic fibrosis. CFTR belongs to the ATP-Binding Cassette (ABC) transporter superfamily, and gating is controlled by phosphorylation and ATP binding and hydrolysis. Recent ATP-free and ATP-bound structures of zebrafish CFTR revealed an unwound segment of transmembrane helix (TM) 8, which appears to be a unique feature of CFTR not present in other ABC transporter structures. Here, by means of 1 μs long molecular dynamics simulations, we investigate the interactions formed by this TM8 segment with nearby helices, in both ATP-free and ATP-bound states. We highlight the structural role of TM8 in maintaining the functional architecture of the pore and we describe a distinct membrane defect that is found near TM8 only in the ATP-free state. The results of the MD simulations are discussed in the context of the gating mechanism of CFTR.

scholarly journals Investigating the effect of Ser256 phosphorylation on gating of aquaporin-2: Molecular Dynamics study

2021 ◽  
Author(s):  
Pragya Priyadarshini ◽  
Balvinder Singh
Keyword(s):  
Molecular Dynamics ◽  
Water Permeability ◽  
Water Movement ◽  
Hydrophobic Interactions ◽  
Md Simulations ◽  
Post Translational Modification ◽  
Functional Changes ◽  
Gating Mechanism ◽  
Intracellular Storage ◽  
Dynamics Simulations

AbstractRegulation of water transport via aquaporins is crucial for osmoregulation and water homeostasis of an organism. This transport of water is regulated either by gating or trafficking wherein AQPs are transported from intracellular storage sites to plasma membrane. It has been proposed that water movement via AQP2 is regulated by post-translational modification. We aimed to explore the structural and functional changes occurring in AQP2 due to Ser256 phosphorylation. We have carried out molecular dynamics simulations to investigate molecular basis of effect of phosphorylation on water permeability of AQP2. MD simulations show that there are mild variations in the pore sizes of different monomers of the phosphorylated and unphosphorylated AQP2. Analysis of inter and intra-monomeric interactions such as hydrogen bond, electrostatic and hydrophobic interactions has been carried out. Structures of the phosphorylated AQP2 do not show any blocking of mouth of pore of the monomers during the course of MD simulations. Further, water permeability calculations do corroborate the above finding. This molecular dynamics study suggests that phosphorylation of C-terminal Ser-256 residue of AQP2 may not be directly responsible for gating mechanism.

scholarly journals The molecular evolution of function in the CFTR chloride channel

2021 ◽  
Vol 153 (12) ◽  
Author(s):  
Daniel T. Infield ◽  
Kerry M. Strickland ◽  
Amit Gaggar ◽  
Nael A. McCarty
Keyword(s):  
Cystic Fibrosis ◽  
Molecular Evolution ◽  
Abc Transporter ◽  
Atp Binding ◽  
Critical Question ◽  
Transport Pathway ◽  
Channel Function ◽  
Domains Of Life ◽  
Bona Fide ◽  
Channel Interactions

The ATP-binding cassette (ABC) transporter superfamily includes many proteins of clinical relevance, with genes expressed in all domains of life. Although most members use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes, the cystic fibrosis transmembrane conductance regulator (CFTR) is the only known animal ABC transporter that functions primarily as an ion channel. Defects in CFTR, which is closely related to ABCC subfamily members that bear function as bona fide transporters, underlie the lethal genetic disease cystic fibrosis. This article seeks to integrate structural, functional, and genomic data to begin to answer the critical question of how the function of CFTR evolved to exhibit regulated channel activity. We highlight several examples wherein preexisting features in ABCC transporters were functionally leveraged as is, or altered by molecular evolution, to ultimately support channel function. This includes features that may underlie (1) construction of an anionic channel pore from an anionic substrate transport pathway, (2) establishment and tuning of phosphoregulation, and (3) optimization of channel function by specialized ligand–channel interactions. We also discuss how divergence and conservation may help elucidate the pharmacology of important CFTR modulators.

Control of the CFTR channel's gates

2005 ◽  
Vol 33 (5) ◽  
pp. 1003-1007 ◽  
Author(s):  
P. Vergani ◽  
C. Basso ◽  
M. Mense ◽  
A.C. Nairn ◽  
D.C. Gadsby
Keyword(s):  
Cystic Fibrosis ◽  
Ion Channel ◽  
Single Channel ◽  
Atp Binding ◽  
Transmembrane Conductance Regulator ◽  
Binding Domains ◽  
Abc Protein ◽  
Channel Opening ◽  
Atp Binding And Hydrolysis ◽  
Opening And Closing

Unique among ABC (ATP-binding cassette) protein family members, CFTR (cystic fibrosis transmembrane conductance regulator), also termed ABCC7, encoded by the gene mutated in cystic fibrosis patients, functions as an ion channel. Opening and closing of its anion-selective pore are linked to ATP binding and hydrolysis at CFTR's two NBDs (nucleotide-binding domains), NBD1 and NBD2. Isolated NBDs of prokaryotic ABC proteins form homodimers upon binding ATP, but separate after hydrolysis of the ATP. By combining mutagenesis with single-channel recording and nucleotide photolabelling on intact CFTR molecules, we relate opening and closing of the channel gates to ATP-mediated events in the NBDs. In particular, we demonstrate that two CFTR residues, predicted to lie on opposite sides of its anticipated NBD1–NBD2 heterodimer interface, are energetically coupled when the channels open but are independent of each other in closed channels. This directly links ATP-driven tight dimerization of CFTR's cytoplasmic NBDs to opening of the ion channel in the transmembrane domains. Evolutionary conservation of the energetically coupled residues in a manner that preserves their ability to form a hydrogen bond argues that this molecular mechanism, involving dynamic restructuring of the NBD dimer interface, is shared by all members of the ABC protein superfamily.

The intact CFTR protein mediates ATPase rather than adenylate kinase activity

2008 ◽  
Vol 412 (2) ◽  
pp. 315-321 ◽  
Author(s):  
Mohabir Ramjeesingh ◽  
Francisca Ugwu ◽  
Fiona L. L. Stratford ◽  
Ling-Jun Huan ◽  
Canhui Li ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Atpase Activity ◽  
Mechanism Of Action ◽  
Adenylate Kinase ◽  
Kinase Activity ◽  
Residual Activity ◽  
Atp Binding ◽  
Cftr Protein ◽  
The Individual ◽  
Atp Binding And Hydrolysis

The two NBDs (nucleotide-binding domains) of ABC (ATP-binding-cassette) proteins function in a complex to mediate ATPase activity and this activity has been linked to their regulated transport activity. A similar model has been proposed for CFTR (cystic fibrosis transmembrane conductance regulator), the chloride channel defective in cystic fibrosis, wherein ATP binding and hydrolysis regulate the channel gate. Recently, it was shown that the individual NBDs isolated from CFTR primarily mediate adenylate kinase activity, raising the possibility that this activity may also contribute to gating of the CFTR channel. However, this present study shows that whereas the isolated NBDs exhibit adenylate kinase activity, the full-length purified and reconstituted CFTR protein functions as an ATPase, arguing that the enzymatic activity of the NBDs is dependent on their molecular context and appropriate domain–domain assembly. As expected, the disease-causing mutant bearing a mutation in the ABC signature motif, CFTR-G551D, exhibited a markedly reduced ATPase activity. Furthermore, mutation of the putative catalytic base in CFTR caused a reduction in ATPase activity, with the CFTR-E1371Q mutant supporting a low level of residual activity. Neither of these mutants exhibited detectable adenylate kinase activity. Together, these findings support the concept that the molecular mechanism of action of CFTR is dependent on ATP binding and hydrolysis, and that the structure of prokaryotic ABC ATPases provide a useful template for understanding their mechanism of action.

scholarly journals Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation

2021 ◽  
Vol 118 (17) ◽  
pp. e2024928118
Author(s):  
Joshua Pajak ◽  
Rockney Atz ◽  
Brendan J. Hilbert ◽  
Marc C. Morais ◽  
Brian A. Kelch ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Signaling Pathway ◽  
Bound States ◽  
Atp Hydrolysis ◽  
Dna Packaging ◽  
Atp Binding ◽  
Dna Translocation ◽  
Viral Packaging ◽  
Mechanochemical Cycle ◽  
Dynamics Simulations

Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors.

scholarly journals Nonequilibrium Gating of CFTR on an Equilibrium Theme

Physiology ◽  
2012 ◽  
Vol 27 (6) ◽  
pp. 351-361 ◽  
Author(s):  
Kang-Yang Jih ◽  
Tzyh-Chang Hwang
Keyword(s):  
Cystic Fibrosis ◽  
Abc Transporter ◽  
Chloride Channel ◽  
Genetic Disease ◽  
Clinical Relevance ◽  
Transmembrane Conductance Regulator ◽  
Transmembrane Conductance ◽  
Abc Protein ◽  
Gating Mechanism ◽  
Cystic Fibrosis Transmembrane

Malfunction of cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ABC protein superfamily that functions as an ATP-gated chloride channel, causes the lethal genetic disease, cystic fibrosis. This review focuses on the most recent findings on the gating mechanism of CFTR. Potential clinical relevance and implications to ABC transporter function are also discussed.

scholarly journals Deciphering collaborative sidechain motions in proteins during molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bruck Taddese ◽  
Antoine Garnier ◽  
Hervé Abdi ◽  
Daniel Henrion ◽  
Marie Chabbert
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Conformational Transition ◽  
Transmembrane Helix ◽  
Principal Component ◽  
Dynamic Structure ◽  
Md Simulations ◽  
Outward Motion ◽  
Dynamics Simulations

Abstract The dynamic structure of proteins is essential for their functions and may include large conformational transitions which can be studied by molecular dynamics (MD) simulations. However, details of these transitions are difficult to automatically track. To facilitate their analysis, we developed two scores of correlation between sidechain dihedral angles. The CIRCULAR and OMES scores are computed from, respectively, dihedral angle values and rotamer distributions. As a case study, we applied our methods to an activation-like transition of the chemokine receptor CXCR4, observed during accelerated MD simulations. The principal component analysis of the correlation matrices was consistent with the networking structure of the top ranking pairs. Both scores identify a set of residues whose “collaborative” sidechain rotamerization immediately preceded or accompanied the conformational transition of CXCR4. Detailed analysis of the sequential order of these rotamerizations suggests that an allosteric mechanism, involving the outward motion of an asparagine residue in transmembrane helix 3, might be a prerequisite to the large scale conformational transition of CXCR4. This case study provides the proof-of-concept that the correlation methods developed here are valuable exploratory techniques to help decipher complex reactional pathways.

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