scholarly journals Phospholamban and sarcolipin share similar transmembrane zipper motifs that control self-association affinity and oligomer stoichiometry

2019 ◽  
Author(s):  
Nicholas R. DesLauriers ◽  
Bengt Svensson ◽  
David D. Thomas ◽  
Joseph M. Autry
Keyword(s):  
Self Assembly ◽  
Resonance Energy ◽  
Higher Order ◽  
Site Directed Mutagenesis ◽  
Heptad Repeat ◽  
Steric Interaction ◽  
Structural Determinants ◽  
Sds Page ◽  
Self Association

AbstractWe have characterized the structural determinants of phospholamban (PLB) and sarcolipin (SLN) self-association using site-directed mutagenesis, SDS-PAGE, and fluorescence resonance energy transfer (FRET) microscopy. PLB and SLN are single-pass transmembrane (TM) peptides that are critically involved in regulation of contractility in cardiac and skeletal muscle via reversible inhibition of calcium (Ca) transport by SERCA. PLB and SLN also exhibit ion channel activity in vitro, yet the physiological significance of these functions is unknown. Here we have determined that structural insights offered by the tetrameric PLB Cys41 to Leu (C41L) mutation, a mutant with four possible leucine/isoleucine zipper interactions for stabilizing PLB tetramers. Using scanning alanine mutagenesis and SDS-PAGE, we have determined the C41L-PLB tetramer is destabilized by mutation of Leu37 to Ala (L37A) or Ile40 to Ala (I40A), which are the same a- and d-arm residues stabilizing the PLB pentamer via leucine/isoleucine zippers, highlighting the importance of these two zippers in PLB higher-order oligomerization. The new possible zipper arm in C41L-PLB (N34, C41L, I48) did not contribute to tetramerization. On the other hand, we determined that tetramer conversion back to pentamer was induced by alanine mutation of Ile48, a residue located on the e-arm below C41L, implicating steric interaction and restriction are the stabilizing and destabilizing forces that control the distribution between pentamer and tetramer populations. We propose that the e-arm and hydrophobic residues in the adjacent b-arm act as secondary structural motifs that help control the stoichiometry of PLB oligomerization. FRET microscopy and alanine mutagenesis of SLN residues Val14 (V14A) or Leu21 (L21A) decreased the binding affinity of the SLN‒SLN complex, demonstrating the importance of each residue in mediating self-association. Helical wheel analysis supports a heptad-repeat TM zipper mechanism of SLN oligomerization, similar to the 3.5 residue/turn Leu and Ile zippers found in PLB pentamers. Collectively, our studies add new insights on the conservation of homologous hydrophobic 3-4 pattern of residues in zipper motifs that mediate PLB and SLN self-assembly. We propose that the importance of these apolar, steric interactions in the TM domain are widespread in stabilizing higher-order oligomerization of membrane proteins.

Programmable in vitro Co-Encapsidation of Guest Proteins Inside Protein Nanocages

2018 ◽  
Author(s):  
Noor H. Dashti ◽  
Rufika S. Abidin ◽  
Frank Sainsbury
Keyword(s):  
Self Assembly ◽  
Mammalian Cells ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Super Resolution ◽  
Cell Engineering ◽  
Particle Analysis ◽  
Protein Cages

Bioinspired self-sorting and self-assembling systems using engineered versions of natural protein cages have been developed for biocatalysis and therapeutic delivery. The packaging and intracellular delivery of guest proteins is of particular interest for both <i>in vitro</i> and <i>in vivo</i> cell engineering. However, there is a lack of platforms in bionanotechnology that combine programmable guest protein encapsidation with efficient intracellular uptake. We report a minimal peptide anchor for <i>in vivo</i> self-sorting of cargo-linked capsomeres of the Murine polyomavirus (MPyV) major coat protein that enables controlled encapsidation of guest proteins by <i>in vitro</i> self-assembly. Using Förster resonance energy transfer (FRET) we demonstrate the flexibility in this system to support co-encapsidation of multiple proteins. Complementing these ensemble measurements with single particle analysis by super-resolution microscopy shows that the stochastic nature of co-encapsidation is an overriding principle. This has implications for the design and deployment of both native and engineered self-sorting encapsulation systems and for the assembly of infectious virions. Taking advantage of the encoded affinity for sialic acids ubiquitously displayed on the surface of mammalian cells, we demonstrate the ability of self-assembled MPyV virus-like particles to mediate efficient delivery of guest proteins to the cytosol of primary human cells. This platform for programmable co-encapsidation and efficient cytosolic delivery of complementary biomolecules therefore has enormous potential in cell engineering.

scholarly journals Higher-order assembly of Sorting Nexin 16 controls tubulation and distribution of neuronal endosomes

2019 ◽  
Vol 218 (8) ◽  
pp. 2600-2618 ◽  
Author(s):  
ShiYu Wang ◽  
Zechuan Zhao ◽  
Avital A. Rodal
Keyword(s):  
Cell Body ◽  
Motor Neurons ◽  
Coiled Coil ◽  
Higher Order ◽  
Synaptic Growth ◽  
Sorting Nexin ◽  
Protein Receptors ◽  
Self Association ◽  
Signaling Receptors

The activities of neuronal signaling receptors depend heavily on the maturation state of the endosomal compartments in which they reside. However, it remains unclear how the distribution of these compartments within the uniquely complex morphology of neurons is regulated and how this distribution itself affects signaling. Here, we identified mechanisms by which Sorting Nexin 16 (SNX16) controls neuronal endosomal maturation and distribution. We found that higher-order assembly of SNX16 via its coiled-coil (CC) domain drives membrane tubulation in vitro and endosome association in cells. In Drosophila melanogaster motor neurons, activation of Rab5 and CC-dependent self-association of SNX16 lead to its endosomal enrichment, accumulation in Rab5- and Rab7-positive tubulated compartments in the cell body, and concomitant depletion of SNX16-positive endosomes from the synapse. This results in accumulation of synaptic growth–promoting bone morphogenetic protein receptors in the cell body and correlates with increased synaptic growth. Our results indicate that Rab regulation of SNX16 assembly controls the endosomal distribution and signaling activities of receptors in neurons.

scholarly journals Calmodulin Binds and Stabilizes the Regulatory Enzyme, CTP:Phosphocholine Cytidylyltransferase

2007 ◽  
Vol 282 (46) ◽  
pp. 33494-33506 ◽  
Author(s):  
Bill. B. Chen ◽  
Rama K. Mallampalli
Keyword(s):  
Animal Cell ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Site Directed Mutagenesis ◽  
Molecular Signature ◽  
Adenoviral Gene Transfer ◽  
Ctp:Phosphocholine Cytidylyltransferase ◽  
Interfering Rna

CTP:phosphocholine cytidylyltransferase (CCTα) is a proteolytically sensitive enzyme essential for production of phosphatidylcholine, the major phospholipid of animal cell membranes. The molecular signals that govern CCTα protein stability are unknown. An NH2-terminal PEST sequence within CCTα did not serve as a degradation signal for the proteinase, calpain. Calmodulin (CaM) stabilized CCTα from calpain proteolysis. Adenoviral gene transfer of CaM in cells protected CCTα, whereas CaM small interfering RNA accentuated CCTα degradation by calpains. CaM bound CCTα as revealed by fluorescence resonance energy transfer and two-hybrid analysis. Mapping and site-directed mutagenesis of CCTα uncovered a motif (LQERVDKVK) harboring a vital recognition site, Gln243, whereby CaM directly binds to the enzyme. Mutagenesis of CCTα Gln243 not only resulted in loss of CaM binding but also led to complete calpain resistance in vitro and in vivo. Thus, calpains and CaM both access CCTα using a structurally similar molecular signature that profoundly affects CCTα levels. These data suggest that CaM, by antagonizing calpain, serves as a novel binding partner for CCTα that stabilizes the enzyme under proinflammatory stress.

Programmable in vitro Co-Encapsidation of Guest Proteins Inside Protein Nanocages

2018 ◽  
Author(s):  
Noor H. Dashti ◽  
Rufika S. Abidin ◽  
Frank Sainsbury
Keyword(s):  
Self Assembly ◽  
Mammalian Cells ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Super Resolution ◽  
Cell Engineering ◽  
Particle Analysis ◽  
Protein Cages

Bioinspired self-sorting and self-assembling systems using engineered versions of natural protein cages have been developed for biocatalysis and therapeutic delivery. The packaging and intracellular delivery of guest proteins is of particular interest for both <i>in vitro</i> and <i>in vivo</i> cell engineering. However, there is a lack of platforms in bionanotechnology that combine programmable guest protein encapsidation with efficient intracellular uptake. We report a minimal peptide anchor for <i>in vivo</i> self-sorting of cargo-linked capsomeres of the Murine polyomavirus (MPyV) major coat protein that enables controlled encapsidation of guest proteins by <i>in vitro</i> self-assembly. Using Förster resonance energy transfer (FRET) we demonstrate the flexibility in this system to support co-encapsidation of multiple proteins. Complementing these ensemble measurements with single particle analysis by super-resolution microscopy shows that the stochastic nature of co-encapsidation is an overriding principle. This has implications for the design and deployment of both native and engineered self-sorting encapsulation systems and for the assembly of infectious virions. Taking advantage of the encoded affinity for sialic acids ubiquitously displayed on the surface of mammalian cells, we demonstrate the ability of self-assembled MPyV virus-like particles to mediate efficient delivery of guest proteins to the cytosol of primary human cells. This platform for programmable co-encapsidation and efficient cytosolic delivery of complementary biomolecules therefore has enormous potential in cell engineering.

scholarly journals An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching

PLoS ONE ◽  
2011 ◽  
Vol 6 (3) ◽  
pp. e17896 ◽  
Author(s):  
Michele L. Markwardt ◽  
Gert-Jan Kremers ◽  
Catherine A. Kraft ◽  
Krishanu Ray ◽  
Paula J. C. Cranfill ◽  
...  
Keyword(s):  
Quantum Yield ◽  
Fluorescence Lifetime ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Living Cells ◽  
Site Directed Mutagenesis ◽  
Quantum Yields

Cyan fluorescent proteins (CFPs), such as Cerulean, are widely used as donor fluorophores in Förster resonance energy transfer (FRET) experiments. Nonetheless, the most widely used variants suffer from drawbacks that include low quantum yields and unstable flurorescence. To improve the fluorescence properties of Cerulean, we used the X-ray structure to rationally target specific amino acids for optimization by site-directed mutagenesis. Optimization of residues in strands 7 and 8 of the β-barrel improved the quantum yield of Cerulean from 0.48 to 0.60. Further optimization by incorporating the wild-type T65S mutation in the chromophore improved the quantum yield to 0.87. This variant, mCerulean3, is 20% brighter and shows greatly reduced fluorescence photoswitching behavior compared to the recently described mTurquoise fluorescent protein in vitro and in living cells. The fluorescence lifetime of mCerulean3 also fits to a single exponential time constant, making mCerulean3 a suitable choice for fluorescence lifetime microscopy experiments. Furthermore, inclusion of mCerulean3 in a fusion protein with mVenus produced FRET ratios with less variance than mTurquoise-containing fusions in living cells. Thus, mCerulean3 is a bright, photostable cyan fluorescent protein which possesses several characteristics that are highly desirable for FRET experiments.

scholarly journals Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

2016 ◽  
Vol 113 (5) ◽  
pp. 1238-1243 ◽  
Author(s):  
Sergei A. Grigoryev ◽  
Gavin Bascom ◽  
Jenna M. Buckwalter ◽  
Michael B. Schubert ◽  
Christopher L. Woodcock ◽  
...  
Keyword(s):  
Strong Dependence ◽  
Eukaryotic Cell ◽  
Higher Order ◽  
Linker Histone ◽  
Cell Nuclei ◽  
Metaphase Chromosomes ◽  
Chromosome Conformation ◽  
Interphase Cell ◽  
Self Association

The architecture of higher-order chromatin in eukaryotic cell nuclei is largely unknown. Here, we use electron microscopy-assisted nucleosome interaction capture (EMANIC) cross-linking experiments in combination with mesoscale chromatin modeling of 96-nucleosome arrays to investigate the internal organization of condensed chromatin in interphase cell nuclei and metaphase chromosomes at nucleosomal resolution. The combined data suggest a novel hierarchical looping model for chromatin higher-order folding, similar to rope flaking used in mountain climbing and rappelling. Not only does such packing help to avoid tangling and self-crossing, it also facilitates rope unraveling. Hierarchical looping is characterized by an increased frequency of higher-order internucleosome contacts for metaphase chromosomes compared with chromatin fibers in vitro and interphase chromatin, with preservation of a dominant two-start zigzag organization associated with the 30-nm fiber. Moreover, the strong dependence of looping on linker histone concentration suggests a hierarchical self-association mechanism of relaxed nucleosome zigzag chains rather than longitudinal compaction as seen in 30-nm fibers. Specifically, concentrations lower than one linker histone per nucleosome promote self-associations and formation of these looped networks of zigzag fibers. The combined experimental and modeling evidence for condensed metaphase chromatin as hierarchical loops and bundles of relaxed zigzag nucleosomal chains rather than randomly coiled threads or straight and stiff helical fibers reconciles aspects of other models for higher-order chromatin structure; it constitutes not only an efficient storage form for the genomic material, consistent with other genome-wide chromosome conformation studies that emphasize looping, but also a convenient organization for local DNA unraveling and genome access.

scholarly journals The Staphylococcal QacR Multidrug Regulator Binds a Correctly Spaced Operator as a Pair of Dimers

2001 ◽  
Vol 183 (24) ◽  
pp. 7102-7109 ◽  
Author(s):  
Steve Grkovic ◽  
Melissa H. Brown ◽  
Maria A. Schumacher ◽  
Richard G. Brennan ◽  
Ronald A. Skurray
Keyword(s):  
Self Assembly ◽  
Degradation Products ◽  
Regulatory Protein ◽  
Gel Filtration ◽  
Site Directed Mutagenesis ◽  
Multidrug Transporter ◽  
Native Form ◽  
Operator Site

ABSTRACT Expression of the Staphylococcus aureusplasmid-encoded QacA multidrug transporter is regulated by the divergently encoded QacR repressor protein. To circumvent the formation of disulfide-bonded degradation products, site-directed mutagenesis to replace the two cysteine residues in wild-type QacR was undertaken. Analysis of a resultant cysteineless QacR derivative indicated that it retained full DNA-binding activities in vivo and in vitro and continued to be fully proficient for the mediation of induction ofqacA expression in response to a range of structurally dissimilar multidrug transporter substrates. The cysteineless QacR protein was used in cross-linking and dynamic light-scattering experiments to show that its native form was a dimer, whereas gel filtration indicated that four QacR molecules bound per DNA operator site. The addition of inducing compounds led to the dissociation of the four operator-bound QacR molecules from the DNA as dimers. Binding of QacR dimers to DNA was found to be dependent on the correct spacing of the operator half-sites. A revised model proposed for the regulation ofqacA expression by QacR features the unusual characteristic of one dimer of the regulatory protein binding to each operator half-site by a process that does not appear to require the prior self-assembly of QacR into tetramers.

scholarly journals Formation of membrane ridges and scallops by the F-BAR protein Nervous Wreck

2013 ◽  
Vol 24 (15) ◽  
pp. 2406-2418 ◽  
Author(s):  
Agata N. Becalska ◽  
Charlotte F. Kelley ◽  
Cristina Berciu ◽  
Tatiana B. Stanishneva-Konovalova ◽  
Xiaofeng Fu ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Higher Order ◽  
Order Structure ◽  
Structural Determinants ◽  
Dynamic Membrane ◽  
Bar Domain ◽  
Neuronal Protein ◽  
Positively Curved

Eukaryotic cells are defined by extensive intracellular compartmentalization, which requires dynamic membrane remodeling. FER/Cip4 homology-Bin/amphiphysin/Rvs (F-BAR) domain family proteins form crescent-shaped dimers, which can bend membranes into buds and tubules of defined geometry and lipid composition. However, these proteins exhibit an unexplained wide diversity of membrane-deforming activities in vitro and functions in vivo. We find that the F-BAR domain of the neuronal protein Nervous Wreck (Nwk) has a novel higher-order structure and membrane-deforming activity that distinguishes it from previously described F-BAR proteins. The Nwk F-BAR domain assembles into zigzags, creating ridges and periodic scallops on membranes in vitro. This activity depends on structural determinants at the tips of the F-BAR dimer and on electrostatic interactions of the membrane with the F-BAR concave surface. In cells, Nwk-induced scallops can be extended by cytoskeletal forces to produce protrusions at the plasma membrane. Our results define a new F-BAR membrane-deforming activity and illustrate a molecular mechanism by which positively curved F-BAR domains can produce a variety of membrane curvatures. These findings expand the repertoire of F-BAR domain mediated membrane deformation and suggest that unique modes of higher-order assembly can define how these proteins sculpt the membrane.

scholarly journals The Synthesis of Protein Polymer Conjugates using the Human Regulatory Protein Galectin-3

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
Ling Lin ◽  
Amanda M. Pritzlaff ◽  
Haillie-Ann C. Lower ◽  
Daniel A. Savin
Keyword(s):  
Ligand Binding ◽  
Regulatory Protein ◽  
Site Directed Mutagenesis ◽  
Galectin 3 ◽  
Self Association ◽  
Lectin Protein ◽  
And Control ◽  
Cancerous Cells

Galectin-3 (gal3) is a human lectin protein that is known to interact with extracellular matrix proteins by regulating functions in both healthy and cancerous cells. The goal of this project is to conjugate polymers to gal3 to better study and control its functions in vitro. We hypothesize that a covalently attached polymer will sterically modulate gal3 function. In the project, we created two protein variants with polymer-reactive handles. The first construct is similar to wild-type gal3 with a cysteine in place of the 6th serine (S6C) which was created by site-directed mutagenesis (SDM). Maleimide-terminated polyethylene oxide (PEO, 5000 g/mol) was then attached to this mutant via thiol-Michael addition at the cysteine site. Attachment of polymer to the unstructured N-terminal domain (NTD) may increase the binding of the protein by sterically pulling the NTD away from the carbohydrate recognition domain (CRD). In addition, the NTD, which is implicated in undesired self-association, was removed for the second construct. The gal3 CRD only construct is shown to have a higher solubility in solution and an increased ligand-binding affinity. Ultimately, the two unique constructs will help us understand the structural role of the NTD in gal3 ligand-binding and self-association.

scholarly journals Extracellular Matrix Determines Biomechanical Properties of Chondrospheres during Their Maturation In Vitro

Cartilage ◽  
2018 ◽  
Vol 11 (4) ◽  
pp. 521-531 ◽  
Author(s):  
Nikolai P. Omelyanenko ◽  
Pavel A. Karalkin ◽  
Elena A. Bulanova ◽  
Elizaveta V. Koudan ◽  
Vladislav A. Parfenov ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Self Assembly ◽  
Biomechanical Properties ◽  
Culture Conditions ◽  
Secant Modulus ◽  
Structural Determinants ◽  
Maturation In Vitro

Objective Chondrospheres represent a variant of tissue spheroids biofabricated from chondrocytes. They are already being used in clinical trials for cartilage repair; however, their biomechanical properties have not been systematically investigated yet. The aim of our study was to characterize chondrospheres in long-term in vitro culture conditions for morphometric changes, biomechanical integrity, and their fusion and spreading kinetics. Results It has been demonstrated that the increase in chondrospheres secant modulus of elasticity is strongly associated with the synthesis and accumulation of extracellular matrix. Additionally, significant interplay has been found between biomechanical properties of tissue spheroids and their fusion kinetics in contrast to their spreading kinetics. Conclusions Extracellular matrix is one of the main structural determinants of chondrospheres biomechanical properties during chondrogenic maturation in vitro. The estimation of tissue spheroids’ physical behavior in vitro prior to operative treatment can be used to predict and potentially control fusogenic self-assembly process after implantation in vivo.

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