scholarly journals Decoupling the ATP-binding Domain in the CheA Kinase by Increasing Linker Flexibility Dramatically Alters Kinase Activity

2021 ◽  
Author(s):  
Zachary Maschmann ◽  
Siddarth Chandrasekaran ◽  
Brian R Crane
Keyword(s):  
Thermotoga Maritima ◽  
Bacterial Chemotaxis ◽  
Helical Structure ◽  
Kinase Domain ◽  
Heptad Repeat ◽  
Binding Affinities ◽  
Dimerization Domain ◽  
Receptor Coupling ◽  
Close Proximity ◽  
Coupling Protein

In bacterial chemotaxis chemoreceptors regulate the cytosolic dimeric histidine kinase CheA. To test the role that interdomain linkers play in CheA regulation the linkers that connect the P4 kinase domain to the P3 dimerization domain (L3) and the P5 regulatory domain (L4) were extended and altered in variants of Thermotoga maritima (Tm) CheA. Flexible extensions of the L3 and L4 linkers in CheA-LV1 (linker variant 1) allow for a well-folded kinase domain that retains WT-like binding affinities for nucleotide and normal interactions with the receptor-coupling protein CheW. However, CheA-LV1 autophosphorylation activity registers ~50-fold lower compared to wild-type. Formation of the CheA-LV1 / CheA WT heterodimer fails to rescue CheA-LV1 autophosphorylation and instead reduces the activity of the WT subunit. Neither CheA WT nor CheA-LV1 can phosphorylate P1 in a CheA dimer that contains a single P4 domain. Rescue of autophosphorylation activity in variants with a poly-alanine L3 or an L3 that maintains a heptad repeat suggest that positioning and conformational transitions of P4 depend on L3 assuming helical structure. Pulse dipolar ESR measurements indicate that the CheA-LV1 P4 domains are in close proximity whereas broader distributions in other variants correlate with increased activity. CheA-LV1 has a substantially larger hydrodynamic radius than does CheA WT by SAXS, despite the P4 domains assuming a closed, inhibited conformation. These results explain negative cooperativity in CheA nucleotide binding, demonstrate coupling between P4 disposition and P1 / P2 dynamics and underscore the importance of P4-P4 interactions and an L3 a- helix in CheA activity and regulation.

scholarly journals Requirement of PKR Dimerization Mediated by Specific Hydrophobic Residues for Its Activation by Double-Stranded RNA and Its Antigrowth Effects in Yeast

1998 ◽  
Vol 18 (12) ◽  
pp. 7009-7019 ◽  
Author(s):  
Rekha C. Patel ◽  
Ganes C. Sen
Keyword(s):  
Helical Structure ◽  
Wild Type ◽  
Dimerization Domain ◽  
Double Stranded Rna ◽  
Mutant Proteins ◽  
Hydrophobic Residues ◽  
Dsrna Binding ◽  
Dependent Protein ◽  
Substitution Mutations

ABSTRACT The roles of protein dimerization and double-stranded RNA (dsRNA) binding in the biochemical and cellular activities of PKR, the dsRNA-dependent protein kinase, were investigated. We have previously shown that both properties of the protein are mediated by the same domain. Here we show that dimerization is mediated by hydrophobic residues present on one side of an amphipathic α-helical structure within this domain. Appropriate substitution mutations of residues on that side produced mutants with increased or decreased dimerization activities. Using these mutants, we demonstrated that dimerization is not essential for dsRNA binding. However, enhancing dimerization artificially, by providing an extraneous dimerization domain, increased dsRNA binding of both wild-type and mutant proteins. In vitro, the dimerization-defective mutants could not be activated by dsRNA but were activated normally by heparin. In Saccharomyces cerevisiae, unlike wild-type PKR, these mutants could not inhibit cell growth and the dsRNA-binding domain of the dimerization-defective mutants could not prevent the antigrowth effect of wild-type PKR. These results demonstrate the biological importance of the dimerization properties of PKR.

scholarly journals Emergence and Evolution of Enfuvirtide Resistance following Long-Term Therapy Involves Heptad Repeat 2 Mutations within gp41

2005 ◽  
Vol 49 (3) ◽  
pp. 1113-1119 ◽  
Author(s):  
L. Xu ◽  
A. Pozniak ◽  
A. Wildfire ◽  
S. A. Stanfield-Oakley ◽  
S. M. Mosier ◽  
...  
Keyword(s):  
Amino Acids ◽  
Heptad Repeat ◽  
Term Therapy ◽  
Compensatory Mutation ◽  
Two Samples ◽  
Close Proximity ◽  
Long Term Therapy ◽  
Changes Over Time ◽  
First Time

ABSTRACT The objective of this study was to track the evolution of sequence changes in both the heptad region 1 (HR1) and HR2 domains of gp41 associated with resistance to enfuvirtide (ENF) in a patient cohort receiving long-term ENF treatment. We studied 17 highly antiretroviral agent-experienced patients receiving long-term ENF treatment with virological rebound or a lack of suppression. Sixty-two samples obtained after between 5 and 107 weeks of ENF therapy were analyzed. Baseline samples from 15 of these 17 patients were available for analysis. Viruses from five samples from four patients were also sequenced after the cessation of ENF therapy. Drug susceptibilities were assessed by a pseudotype virus reporter assay. We identified HR1 and HR2 sequence changes over time in relation to the baseline sequences. Mutations in HR1 (amino acids 36 to 45) were noted in all cases, including previously unreported changes N42Q/H and N43Q. In addition to a range of HR2 sequence changes at polymorphic sites, isolates from 6 of 17 (35%) patients developed an S138A substitution in the HR2 domain at least 8 weeks after the start of ENF treatment and also subsequent to the first emergence of HR1 mutations. In most, but not all, cases the S138A mutation accompanied HR1 mutations at position 43. Molecular modeling demonstrates the close proximity of S138A with amino acids 40 and 45 in HR1. Of note, isolates in samples available from four patients demonstrated the loss of both the HR1 and the S138A HR2 mutations following the cessation of therapy. We show that the S138A HR2 mutation increased the level of resistance by approximately threefold over that conferred by the HR1 mutation N43D. Continual evolution of HR1 in the domain from amino acids 36 to 45 was observed during long-term ENF therapy. We have identified, for the first time, an ENF resistance-associated HR2 mutation, S138A, which appeared in isolates from 6 of 17 patients with virological failure and demonstrated its potential to contribute to drug resistance. We propose that this represents a possible secondary and/or compensatory mutation, particularly when it coexists with mutations at position 43 in HR-1.

scholarly journals The tRNA-binding moiety in GCN2 contains a dimerization domain that interacts with the kinase domain and is required for tRNA binding and kinase activation

2001 ◽  
Vol 20 (6) ◽  
pp. 1425-1438 ◽  
Author(s):  
Hongfang Qiu ◽  
Jinsheng Dong ◽  
Cuihua Hu ◽  
Christopher S. Francklyn ◽  
Alan G. Hinnebusch
Keyword(s):  
Kinase Domain ◽  
Dimerization Domain ◽  
Kinase Activation ◽  
Trna Binding

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 Atypical chemoreceptor arrays accommodate high membrane curvature

2020 ◽  
Author(s):  
Alise R. Muok ◽  
Davi R. Ortega ◽  
Kurni Kurniyati ◽  
Wen Yang ◽  
Adam Sidi Mabrouk ◽  
...  
Keyword(s):  
Oxygen Sensor ◽  
Membrane Curvature ◽  
Model Organisms ◽  
Treponema Denticola ◽  
Signaling System ◽  
Dimerization Domain ◽  
Coupling Protein ◽  
Chemotaxis System ◽  
First Time

Abstract/SummaryThe prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology, but most insights have been obtained from only a few model organisms and many studies have relied on artificial systems that alter membrane curvature1–3. In all previously described species, chemoreceptors organize with the histidine kinase (CheA) and coupling protein (CheW) into a hexagonal (P6 symmetry) extended array that is considered universal among archaea and bacteria4,5. Here, for the first time, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that the Td chemoreceptor arrays assume a truly unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several additional atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus in an extremely curved cell. Furthermore, the previously characterized Td oxygen sensor ODP influences array integrity and its loss substantially orders CheA. These results suggest a greater diversity of the chemotaxis signaling system than previously thought and demonstrate the importance of examining transmembrane systems in vivo to retain native membrane curvature.

KIF5B-RET: Discovery of a novel fusion oncogene in lung adenocarcinomas by a systematic screen for tyrosine kinase fusions and identification of patients for a RET targeted therapy trial.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 7578-7578
Author(s):  
Yoshiyuki Suehara ◽  
Maria E. Arcila ◽  
Alexander Edward Dela Cruz Drilon ◽  
Tatsuo Ito ◽  
Lu Wang ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Kinase Domain ◽  
Positive Sample ◽  
The Novel ◽  
Rt Pcr ◽  
Dimerization Domain ◽  
Phase 2 Trial ◽  
Related Variant ◽  
Rapid Amplification ◽  
Lung Adenocarcinomas

7578 Background: The mutually exclusive pattern of major targetable driver oncogenes in lung adenocarcinomas (ADC) suggests that other similar driver oncogenes may exist. We therefore performed a systematic screen for tyrosine kinase (TK) fusions in cases without known driver oncogenes by measuring aberrantly high RNA expression of kinase domain (KD) exons relative to more 5’ exons. Methods: We studied 74 patients whose lung ADC lacked mutations in KRAS, EGFR, BRAF, HER2, and ALK fusions. A NanoString-based assay was designed to query the transcripts of 90 TKs at two points: 5’ to the KD and within or 3’ to the KD. Tumor RNAs were hybridized to the NanoString probes and analyzed for outlier 3’ to 5’ expression ratios. The assay was validated on samples with known ALK and ROS fusions. Presumed novel fusion events were followed up by rapid amplification of cDNA ends (RACE) and confirmatory RT-PCR. Results: The NanoString assay identified aberrant 5’ to 3’ ratios in ROS and RET in 2 cases, respectively, out of 74. RACE analysis isolated a novel GOPC-ROS fusion in the former and a novel KIF5B-RET fusion in the latter, both confirmed by RT-PCR. Further screening by RT-PCR for KIF5B-RET identified one more positive sample in the study set that had not been detected by NanoString. At the RNA level, both fusions joined exon 15 of KIF5B to exon 12 of RET, thus retaining a portion of the dimerization domain of KIF5B and the entire KD of RET, analogous to RET fusions in papillary thyroid carcinoma (TC). One KIF5B-RET patient was a 60 y.o. female never smoker, the other, a 73 y.o. male former smoker. Conclusions: The novel KIF5B-RET fusion described here and also recently reported by Ju YS et al. (Genome Res, Dec 22, 2011) defines a new subset of lung ADC with a potentially targetable driver oncogene. Based on these genetic data and the preclinical activity of the RET inhibitor XL184 (Exelixis) in papillary TC and its known activity in medullary TC with RET mutations, we have initiated prospective testing for KIF5B-RET as part of our lung ADC screening panel in anticipation of a planned phase 2 trial with XL184 in patients with KIF5B-RET or related variant RET fusions.

Activating Mutation in the Catalytic Domain of c-kit Elicits Hematopoietic Transformation by Receptor Self-Association Not at the Ligand-Induced Dimerization Site

Blood ◽  
1999 ◽  
Vol 93 (4) ◽  
pp. 1319-1329 ◽  
Author(s):  
Tohru Tsujimura ◽  
Koji Hashimoto ◽  
Hitoshi Kitayama ◽  
Hirokazu Ikeda ◽  
Hiroyuki Sugahara ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Catalytic Domain ◽  
Extracellular Domain ◽  
Kinase Domain ◽  
Dominant Negative ◽  
Juxtamembrane Domain ◽  
Dimerization Domain ◽  
Receptor Dimerization ◽  
Activating Mutation ◽  
Self Association

The c-kit receptor tyrosine kinase (KIT) is constitutively activated by naturally occurring mutations in either the juxtamembrane domain or the kinase domain. Although the juxtamembrane domain mutations led to ligand-independent KIT dimerization, the kinase domain mutations (Asp814 → Val or Tyr) did not. In an effort to determine if the kinase domain mutant could transfer oncogenic signaling without receptor dimerization, we have constructed the truncated types of c-kitWild and c-kitTyr814 cDNAs (c-kitDel-Wild and c-kitDel-Tyr814 cDNAs, respectively), in which ligand-binding and ligand-induced dimerization domains were deleted. When c-kitDel-Wild and c-kitDel-Tyr814 genes were introduced into a murine interleukin-3 (IL-3)–dependent cell line Ba/F3, KITDel-Tyr814 was constitutively phosphorylated on tyrosine and activated, whereas KITDel-Wild was not. In addition, Ba/F3 cells expressing KITDel-Tyr814(Ba/F3Del-Tyr814) grew in suspension culture without the addition of exogenous growth factor, whereas Ba/F3 cells expressing KITDel-Wild (Ba/F3Del-Wild) required IL-3 for growth. The factor-independent growth of Ba/F3Del-Tyr814 cells was virtually abrogated by coexpression of KITW42 that is a dominant-negative form of KIT, but not by that of KITWild, suggesting that KITDel-Tyr814 may not function as a monomer but may require receptor dimerization for inducing factor-independent growth. Furthermore, KITDel-Tyr814 was found to be coimmunoprecipitated with KITWild or KITW42 by an ACK2 monoclonal antibody directed against the extracellular domain of KIT. Moreover, KITW42 was constitutively associated with a chimeric FMS/KITTyr814 receptor containing the ligand-binding and receptor dimerization domain of c-fmsreceptor (FMS) fused to the transmembrane and cytoplasmic domain of KITTyr814, but not with a chimeric FMS/KITWildreceptor even after stimulation with FMS-ligand. These results suggest that constitutively activating mutation of c-kit at the Asp814 codon may cause a conformation change that leads to receptor self-association not in the extracellular domain and that the receptor self-association of the Asp814 mutant may be important for activation of downstream effectors that are required for factor-independent growth and tumorigenicity.

scholarly journals Extremely Thermostabilizing Core Mutations in Coiled-Coil Mimetic Proteins of HIV-1 gp41 Produce Diverse Effects on Target Binding but Do Not Affect Their Inhibitory Activity

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 566
Author(s):  
Mario Cano-Muñoz ◽  
Samuele Cesaro ◽  
Bertrand Morel ◽  
Julie Lucas ◽  
Christiane Moog ◽  
...  
Keyword(s):  
Inhibitory Activity ◽  
Coiled Coil ◽  
Helical Structure ◽  
Heptad Repeat ◽  
Single Chain ◽  
Cell Infection ◽  
Polar Residues ◽  
Hiv 1

A promising strategy to neutralize HIV-1 is to target the gp41 spike subunit to block membrane fusion with the cell. We previously designed a series of single-chain proteins (named covNHR) that mimic the trimeric coiled-coil structure of the gp41 N-terminal heptad repeat (NHR) region and potently inhibit HIV-1 cell infection by avidly binding the complementary C-terminal heptad repeat (CHR) region. These proteins constitute excellent tools to understand the structural and thermodynamic features of this therapeutically important interaction. Gp41, as with many coiled-coil proteins, contains in core positions of the NHR trimer several highly conserved, buried polar residues, the role of which in gp41 structure and function is unclear. Here we produced three covNHR mutants by substituting each triad of polar residues for the canonical isoleucine. The mutants preserve their helical structure and show an extremely increased thermal stability. However, increased hydrophobicity enhances their self-association. Calorimetric analyses show a marked influence of mutations on the binding thermodynamics of CHR-derived peptides. The mutations do not affect however the in vitro HIV-1 inhibitory activity of the proteins. The results support a role of buried core polar residues in maintaining structural uniqueness and promoting an energetic coupling between conformational stability and NHR–CHR binding.

scholarly journals Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters

2006 ◽  
Vol 90 (12) ◽  
pp. 4317-4326 ◽  
Author(s):  
Monica L. Skoge ◽  
Robert G. Endres ◽  
Ned S. Wingreen
Keyword(s):  
Bacterial Chemotaxis ◽  
Coupled Clusters ◽  
Strongly Coupled ◽  
Receptor Coupling

scholarly journals Identification of Methylation Sites in Thermotoga maritima Chemotaxis Receptors

2006 ◽  
Vol 188 (11) ◽  
pp. 4093-4100 ◽  
Author(s):  
Eduardo Perez ◽  
Haiyan Zheng ◽  
Ann M. Stock
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Thermotoga Maritima ◽  
Consensus Sequence ◽  
Bacterial Chemotaxis ◽  
Cytoplasmic Domains ◽  
Consensus Sequences ◽  
Chemotaxis Proteins ◽  
Chemotaxis Receptors

ABSTRACT Adaptation in bacterial chemotaxis involves reversible methylation of specific glutamate residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins. The specific sites of methylation in Salmonella enterica and Escherichia coli chemoreceptors, identified 2 decades ago, established a consensus sequence for methylation by methyltransferase CheR. Here we report the in vitro methylation of chemoreceptors from Thermotoga maritima, a hyperthermophile that has served as a useful source of chemotaxis proteins for structural analysis. Sites of methylation have been identified by liquid chromatography-mass spectrometry/mass spectrometry. Fifteen sites of methylation were identified within the cytoplasmic domains of four different T. maritima chemoreceptors. The results establish a consensus sequence for chemoreceptor methylation sites in T. maritima that is distinct from the previously identified consensus sequence for E. coli and S. enterica. These findings suggest that consensus sequences for posttranslational modifications in one organism may not be directly extrapolated to analogous modifications in other bacteria.

Sign in / Sign up

Export Citation Format

Share Document