scholarly journals Recognition and targeting mechanisms by chaperones in flagellum assembly and operation

2016 ◽  
Vol 113 (35) ◽  
pp. 9798-9803 ◽  
Author(s):  
Nandish Khanra ◽  
Paolo Rossi ◽  
Anastassios Economou ◽  
Charalampos G. Kalodimos
Keyword(s):  
Membrane Protein ◽  
Binding Sites ◽  
Solution Structure ◽  
Hydrophobic Surface ◽  
The Other ◽  
Capping Protein ◽  
Substrate Complex ◽  
Substrate Protein ◽  
Flagellar Proteins ◽  
Substrate Proteins

The flagellum is a complex bacterial nanomachine that requires the proper assembly of several different proteins for its function. Dedicated chaperones are central in preventing aggregation or undesired interactions of flagellar proteins, including their targeting to the export gate. FliT is a key flagellar chaperone that binds to several flagellar proteins in the cytoplasm, including its cognate filament-capping protein FliD. We have determined the solution structure of the FliT chaperone in the free state and in complex with FliD and the flagellar ATPase FliI. FliT adopts a four-helix bundle and uses a hydrophobic surface formed by the first three helices to recognize its substrate proteins. We show that the fourth helix constitutes the binding site for FlhA, a membrane protein at the export gate. In the absence of a substrate protein FliT adopts an autoinhibited structure wherein both the binding sites for substrates and FlhA are occluded. Substrate binding to FliT activates the complex for FlhA binding and thus targeting of the chaperone–substrate complex to the export gate. The activation and targeting mechanisms reported for FliT appear to be shared among the other flagellar chaperones.

scholarly journals DegSampler: Gibbs sampling strategy for predicting E3-binding sites with position-specific prior information

2020 ◽  
Author(s):  
Osamu Maruyama ◽  
Fumiko Matsuzaki
Keyword(s):  
Gibbs Sampling ◽  
Binding Sites ◽  
Motif Discovery ◽  
Sampling Strategy ◽  
Ubiquitin Proteasome System ◽  
Cellular Processes ◽  
Substrate Protein ◽  
Region Data ◽  
Gibbs Sampling Algorithm ◽  
Substrate Proteins

Abstract Background: The ubiquitin-proteasome system is a pathway in eukaryotic cells for degrading polyubiquitin-tagged proteins through the proteasomal machinery to control various cellular processes and maintain intracellular homeostasis. In this system, the E3 ubiquitin ligase (hereinafter E3) plays an important role in selectively recognizing and binding to specific regions of its substrate proteins. The relationship between a substrate protein and its sites bound by E3s is not well understood. Thus, it is challenging to computationally identify such sites in substrate proteins. Results: In this study, we proposed a collapsed Gibbs sampling algorithm called DegSampler (Degron Sampler) to identify the binding sites of E3s. DegSampler employs a position-specific prior probability distribution, based on the estimated information of the disorder-to-order region bound by any protein. Conclusions: Our computational experiments show that DegSampler achieved 5 and 3.5 times higher the F-measure values of MEME and GLAM2, respectively. Thus DegSampler is the first model demonstrating an effective way of using estimated information on disorder-to-order binding regions in motif discovery. We expect our results to improve further as higher quality proteome-wide disorder-to-order binding region data become available.

THE MOLECULAR ORGANIZATION OF HUMAN ALPHA 2-MACROGLOBULIN. AN IMMUNO ELECTRON MICROSCOPIC STUDY WITH MONOCLONAL ANTIBODIES

1987 ◽  
Author(s):  
E Delain ◽  
M Barrav ◽  
J Tapon-Bretaudière ◽  
F Pochon ◽  
F Van Leuven
Keyword(s):  
Monoclonal Antibodies ◽  
Binding Sites ◽  
Divalent Cations ◽  
The Other ◽  
Molecular Organization ◽  
Cellular Receptor ◽  
Electron Microscopic ◽  
Microscopic Method ◽  
Bait Region ◽  
Electron Microscopic Method

Electron microscopy is a very convenient method to localize the epitopes of monoclonal antibodies (mAbs) at the surface of macromolecules for studying their tree-dimensional organization.We applied this immuno-electron microscopic method to human ct2-macroglobulin (ct2M). 29 anti-α2M mAbs have been tested with the four different forms of a2M : native and chymotrypsin-transformed tetramers, and the corresponding dimers, obtained by dissociation with divalent cations. These mAbs can be classified in three types : those which are specific for 1) the H-like transformed molecules, 2) the native molecules, and 3) those which can react with both forms of α2M.1) Among the H-like α2M specific mAbs, several react with the 20 kD-domain which is recognized by the cellular receptor of transformed a2M. This domain is located at the carboxyterminal end of each monomer. One IgG binds to the end of two adjacent tips of the H-like form.The other mAbs of this type bind to the α2M tips at non-terminal positions. Intermolecular connections built polymers of alternating α2M and IgG molecules.2) Among the native a2M-specific mAbs some are able to inhibit the protease-induced transformation of the native α2M. The binding sites of these mAbs are demonstrated on the native half-molecules. One of these mAbs was also able to react with transformed dimers, in a region corresponding very likely to an inaccessible epitope in the tetrameric transformed α2M molecule.3) Among the mAbs of this type, only two were able to inhibit the protease-induced transformation of α2M. Obviously, their epitopes should be close to the bait region of α2M. The other mAbs reacting with both α2M forms did not inhibit the α2M transformation.All these mAbs can be distinguished by the structure of the immune complexes formed with all forms of α2M. The epitopes are more easily located on the dimers and on the H-like transformed α2M than on the native molecules.From these observations, we propose a new model of the tree-dimensional organization of the human α2M in its native and transformed configurations, and of its protease-induced transformation.

scholarly journals Novel Interactions of ESCRT-III with LIP5 and VPS4 and their Implications for ESCRT-III Disassembly

2008 ◽  
Vol 19 (6) ◽  
pp. 2661-2672 ◽  
Author(s):  
Soomin Shim ◽  
Samuel A. Merrill ◽  
Phyllis I. Hanson
Keyword(s):  
Atpase Activity ◽  
Binding Site ◽  
Binding Sites ◽  
Essential Role ◽  
Multivesicular Body ◽  
The Other ◽  
Aaa Atpase ◽  
Direct Binding ◽  
Novel Interactions

The AAA+ ATPase VPS4 plays an essential role in multivesicular body biogenesis and is thought to act by disassembling ESCRT-III complexes. VPS4 oligomerization and ATPase activity are promoted by binding to LIP5. LIP5 also binds to the ESCRT-III like protein CHMP5/hVps60, but how this affects its function remains unclear. Here we confirm that LIP5 binds tightly to CHMP5, but also find that it binds well to additional ESCRT-III proteins including CHMP1B, CHMP2A/hVps2–1, and CHMP3/hVps24 but not CHMP4A/hSnf7–1 or CHMP6/hVps20. LIP5 binds to a different region within CHMP5 than within the other ESCRT-III proteins. In CHMP1B and CHMP2A, its binding site encompasses sequences at the proteins' extreme C-termini that overlap with “MIT interacting motifs” (MIMs) known to bind to VPS4. We find unexpected evidence of a second conserved binding site for VPS4 in CHMP2A and CHMP1B, suggesting that LIP5 and VPS4 may bind simultaneously to these proteins despite the overlap in their primary binding sites. Finally, LIP5 binds preferentially to soluble CHMP5 but instead to polymerized CHMP2A, suggesting that the newly defined interactions between LIP5 and ESCRT-III proteins may be regulated by ESCRT-III conformation. These studies point to a role for direct binding between LIP5 and ESCRT-III proteins that is likely to complement LIP5's previously described ability to regulate VPS4 activity.

Cell adhesion and phagocytosis promoted by monoclonal antibodies not directed against fibronectin receptors

1988 ◽  
Vol 90 (2) ◽  
pp. 201-214 ◽  
Author(s):  
F. Grinnell ◽  
C.H. Ho ◽  
T.L. Tuan
Keyword(s):  
Monoclonal Antibodies ◽  
Cell Adhesion ◽  
Binding Sites ◽  
Cell Spreading ◽  
The Other ◽  
Immunofluorescence Staining ◽  
Baby Hamster Kidney ◽  
Bhk Cells ◽  
Reducing Conditions ◽  
Latex Beads

In this report we describe cell adhesion and phagocytosis promoted by two monoclonal antibodies that were selected for immunofluorescence staining of non-permeabilized baby hamster kidney (BHK) cells. Anti-BHK1 staining was heaviest along cell margins, whereas anti-BHK2 staining was continuous along cell margins. Neither antibody stained elongated plaque structures such as were observed when cells were reacted with antibodies to fibronectin (FN) receptors. The monoclonal antibodies functioned as adhesion ligands in four different assays: attachment to culture dishes, spreading, binding of latex beads and phagocytosis. Anti-BHK1 and anti-BHK2 promoted attachment to culture dishes similarly, but anti-BHK2 was more effective at promoting cell spreading. Antibody-promoted cell spreading was inhibited by the peptides Ser-Asp-Gly-Arg and Gly-Arg-Gly-Asp-Ser-Pro but not by other, related, peptides tested. The monoclonal antibodies also promoted binding of latex beads, and the bead binding sites were motile, on the basis of their ‘capping’ response. Nevertheless, anti-BHK2 beads were phagocytosed by cells 5- to 20-fold more efficiently than anti-BHK1 beads. The binding sites for anti-BHK1 and anti-BHK2 were characterized by immunoprecipitation experiments. Anti-BHK1 binding sites contained 50K (K = 10(3) Mr) and 88K components under non-reducing conditions that migrated as a 51/53K doublet and a 93K component under reducing conditions. On the other hand, anti-BHK2 binding sites contained 88K and 110K components under non-reducing conditions that shifted to apparent 107K and 128K values when measured under reducing conditions.

The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers

1989 ◽  
Vol 9 (11) ◽  
pp. 4621-4630
Author(s):  
D J Mahoney ◽  
J R Broach
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Binding Sites ◽  
The Other ◽  
Functional Domains ◽  
Gene Products ◽  
Cis Acting ◽  
Full Expression ◽  
Mating Type Genes ◽  
Chromosome Iii

Mating-type genes resident in the silent cassette HML at the left arm of chromosome III are repressed by the action of four SIR gene products, most likely mediated through two cis-acting sites located on opposite sides of the locus. We showed that deletion of either of these two cis-acting sites from the chromosome did not yield any detectable derepression of HML, while deletion of both sites yielded full expression of the locus. In addition, each of these sites was capable of exerting repression of heterologous genes inserted in their vicinity. Thus, HML expression is regulated by two independent silencers, each fully competent for maintaining repression. This situation was distinct from the organization of the other silent locus, HMR, at which a single silencer served as the predominant repressor of expression. Examination of identifiable domains and binding sites within the HML silencers suggested that silencing activity can be achieved by a variety of combinations of various functional domains.

Chemotaxis-associated properties of separated prestalk and prespore cells of Dictyostelium discoideum

1986 ◽  
Vol 64 (8) ◽  
pp. 722-732 ◽  
Author(s):  
J. D. Mee ◽  
D. M. Tortolo ◽  
M. B. Coukell
Keyword(s):  
Light Scattering ◽  
Cell Surface ◽  
Dictyostelium Discoideum ◽  
Binding Sites ◽  
Large Fraction ◽  
Cell Types ◽  
The Other ◽  
Deficient Mutant ◽  
Camp Phosphodiesterase ◽  
Intracellular Cgmp

During development, prestalk and prespore cells of Dictyostelium discoideum become organized in multicellular structures. This physical association makes it difficult to characterize the two cell types biochemically and physiologically. In the present study, we have separated prestalk and prespore cells from 16-h slugs by the method of Tsang and Bradbury and have examined a number of chemotaxis-associated properties of these cells. When assayed on phosphate-buffered agar under both gradient and nongradient conditions, isolated prestalk cells responded chemotactically to cAMP and, unexpectedly, to folate and certain folate derivatives. In contrast, separated prespore cells failed to respond appreciably to any of these compounds. Neither prestalk nor prespore cells of strain HC91 exhibited a cAMP-induced increase in intracellular cGMP. However, a cGMP response was observed in both prestalk and prespore cells of strain NP368, a cGMP phosphodiesterase deficient mutant. Both cell types exhibited comparable cAMP-mediated light-scattering changes and possessed similar levels of surface cAMP- and folate-binding sites. On the other hand, prestalk cells had at least fourfold higher cAMP phosphodiesterase and folate deaminase activities than prespore cells, and a large fraction of both activities was on the cell surface. Therefore, the greater chemotactic response of prestalk cells to cAMP and folate on agar might be due, in part, to their increased capacity to generate a chemoattractant gradient. Results obtained in this study demonstrate that prestalk and prespore cells separated by this procedure can be used in certain physiological as well as biochemical experiments.

scholarly journals The structure of the native cardiac thin filament at systolic Ca2+ levels

2021 ◽  
Vol 118 (13) ◽  
pp. e2024288118
Author(s):  
Cristina M. Risi ◽  
Ian Pepper ◽  
Betty Belknap ◽  
Maicon Landim-Vieira ◽  
Howard D. White ◽  
...  
Keyword(s):  
Cardiac Muscle ◽  
Binding Sites ◽  
Short Range ◽  
Bound States ◽  
Thin Filament ◽  
Narrow Range ◽  
The Other ◽  
Thin Filaments ◽  
Troponin Complex ◽  
Myosin Binding

Every heartbeat relies on cyclical interactions between myosin thick and actin thin filaments orchestrated by rising and falling Ca2+ levels. Thin filaments are comprised of two actin strands, each harboring equally separated troponin complexes, which bind Ca2+ to move tropomyosin cables away from the myosin binding sites and, thus, activate systolic contraction. Recently, structures of thin filaments obtained at low (pCa ∼9) or high (pCa ∼3) Ca2+ levels revealed the transition between the Ca2+-free and Ca2+-bound states. However, in working cardiac muscle, Ca2+ levels fluctuate at intermediate values between pCa ∼6 and pCa ∼7. The structure of the thin filament at physiological Ca2+ levels is unknown. We used cryoelectron microscopy and statistical analysis to reveal the structure of the cardiac thin filament at systolic pCa = 5.8. We show that the two strands of the thin filament consist of a mixture of regulatory units, which are composed of Ca2+-free, Ca2+-bound, or mixed (e.g., Ca2+ free on one side and Ca2+ bound on the other side) troponin complexes. We traced troponin complex conformations along and across individual thin filaments to directly determine the structural composition of the cardiac native thin filament at systolic Ca2+ levels. We demonstrate that the two thin filament strands are activated stochastically with short-range cooperativity evident only on one of the two strands. Our findings suggest a mechanism by which cardiac muscle is regulated by narrow range Ca2+ fluctuations.

scholarly journals Contributions of UP Elements and the Transcription Factor FIS to Expression from the Seven rrn P1 Promoters inEscherichia coli

2001 ◽  
Vol 183 (21) ◽  
pp. 6305-6314 ◽  
Author(s):  
Christine A. Hirvonen ◽  
Wilma Ross ◽  
Christopher E. Wozniak ◽  
Erin Marasco ◽  
Jennifer R. Anthony ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Activity ◽  
The Other ◽  
Multigene Families ◽  
Inescherichia Coli ◽  
Start Site ◽  
Transcription Start ◽  
Control Of Gene Expression ◽  
Up Elements

ABSTRACT The high activity of the rrnB P1 promoter inEscherichia coli results from acis-acting DNA sequence, the UP element, and atrans-acting transcription factor, FIS. In this study, we examine the effects of FIS and the UP element at the other sixrrn P1 promoters. We find that UP elements are present at all of the rrn P1 promoters, but they make different relative contributions to promoter activity. Similarly, FIS binds upstream of, and activates, all seven rrn P1 promoters but to different extents. The total number of FIS binding sites, as well as their positions relative to the transcription start site, differ at each rrn P1 promoter. Surprisingly, the FIS sites upstream of site I play a much larger role in transcription from most rrn P1 promoters compared to rrnBP1. Our studies indicate that the overall activities of the sevenrrn P1 promoters are similar, and the same contributors are responsible for these high activities, but these inputs make different relative contributions and may act through slightly different mechanisms at each promoter. These studies have implications for the control of gene expression of unlinked multigene families.

Outer Membrane Protein Composition in Disease Isolates of Haemophilus influenzae : Pathogenic and Epidemiological Implications

1980 ◽  
Vol 30 (3) ◽  
pp. 709-717
Author(s):  
Marilyn R. Loeb ◽  
David H. Smith
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Haemophilus Influenzae ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Outer Membrane Proteins ◽  
Protein Composition ◽  
The Other ◽  
Major Protein ◽  
Single Strain

The outer membrane protein composition of 50 disease isolates of Haemophilus influenzae has been determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. All strains, including 28 strains of serotype b , one strain each of serotypes a, c, d, e , and f , and 17 untypable strains, had an outer membrane protein composition typical of gram-negative bacteria, i.e., these membranes contained two to three dozen proteins with four to six proteins accounting for most of their protein content. Variation in the mobility of these major outer membrane proteins from strain to strain was common but not universal; the observed patterns provided useful data and new insight into the epidemiology of type b disease. The basic findings can be summarized as follows: (i) All 50 strains possessed three proteins (one minor and two major) each having identical mobilities. The other proteins, both major and minor, varied in mobility. (ii) All type b strains possessed a fourth (major) protein of identical mobility. (iii) The 28 type b strains, on the basis of the mobility of the six major outer membrane proteins, could be divided into eight subtypes. Of all the other strains examined, both typable and untypable, only the serotype a strain belonged to one of these subtypes. (iv) The untypable strains showed considerable variation in the mobilities of their major outer membrane proteins. Of these 17 strains, 13 had an additional major outer membrane protein not present in encapsulated strains. (v) The outer membrane protein composition of a single strain remained unchanged after many passages on solid media, but varied with the growth phase. (vi) The outer membrane protein composition of isolates obtained from nine patients during an epidemic of type b meningitis varied, indicating that a single strain was not responsible for the epidemic. At least five different strains were responsible for these nine cases. (vii) Identical outer membrane protein compositions were observed in the following: in a type b strain and a mutant of this strain deficient in capsule production, indicating that the level of capsule synthesis is not obviously related to outer membrane protein composition; in type b strains isolated from different anatomic sites of patients acutely ill with meningitis, indicating that the strain associated with bacteremia is the same as that isolated from the cerebrospinal fluid; in type b strains isolated from siblings who contracted meningitis at about the same time, indicating infection with the same strain; and in type b strains isolated from the initial and repeat infection of a single patient, suggesting that reinfection was due to the same strain.

E-box- and MEF-2-independent muscle-specific expression, positive autoregulation, and cross-activation of the chicken MyoD (CMD1) promoter reveal an indirect regulatory pathway

1994 ◽  
Vol 14 (8) ◽  
pp. 5474-5486
Author(s):  
C A Dechesne ◽  
Q Wei ◽  
J Eldridge ◽  
L Gannoun-Zaki ◽  
P Millasseau ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Primary Cultures ◽  
Regulatory Elements ◽  
The Other ◽  
Indirect Pathway ◽  
Specific Expression ◽  
Fibroblast Cultures ◽  
E Box ◽  
Myogenic Factors

Members of the MyoD family of gene-regulatory proteins (MyoD, myogenin, myf5, and MRF4) have all been shown not only to regulate the transcription of numerous muscle-specific genes but also to positively autoregulate and cross activate each other's transcription. In the case of muscle-specific genes, this transcriptional regulation can often be correlated with the presence of a DNA consensus in the regulatory region CANNTG, known as an E box. Little is known about the regulatory interactions of the myogenic factors themselves; however, these interactions are thought to be important for the activation and maintenance of the muscle phenotype. We have identified the minimal region in the chicken MyoD (CMD1) promoter necessary for muscle-specific transcription in primary cultures of embryonic chicken skeletal muscle. The CMD1 promoter is silent in primary chick fibroblast cultures and in muscle cell cultures treated with the thymidine analog bromodeoxyuridine. However, CMD1 and chicken myogenin, as well as, to a lesser degree, chicken Myf5 and MRF4, expressed in trans can activate transcription from the minimal CMD1 promoter in these primary fibroblast cultures. Here we show that the CMD1 promoter contains numerous E-box binding sites for CMD1 and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific expression, autoregulation, or cross activation depends upon the presence of of these E-box or MEF-2 binding sites in the CMD1 promoter. These results demonstrate that the autoregulation and cross activation of the chicken MyoD promoter through the putative direct binding of the myogenic basic helix-loop-helix regulatory factors is mediated through an indirect pathway that involves unidentified regulatory elements and/or ancillary factors.

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