scholarly journals A novel domain assembly routine for creating full-length models of membrane proteins from known domain structures

2017 ◽  
Author(s):  
Julia Koehler Leman ◽  
Richard Bonneau
Keyword(s):  
Membrane Proteins ◽  
Biological Function ◽  
Transmembrane Domain ◽  
Search Space ◽  
Full Length ◽  
Conformational Search ◽  
Membrane Domains ◽  
Native Structure ◽  
Domain Structures ◽  
Fragment Insertion

AbstractMembrane proteins composed of soluble and membrane domains are often studied one domain at a time. However, to understand the biological function of entire protein systems and their interactions with each other and drugs, knowledge of full-length structures or models is required. Although few computational methods exist that could potentially be used to model full-length constructs of membrane proteins, none of these methods are perfectly suited for the problem at hand. Existing methods either require an interface or knowledge of the relative orientations of the domains, are not designed for domain assembly, and none of them are developed for membrane proteins. Here we describe the first domain assembly protocol specifically designed for membrane proteins that assembles intra- and extracellular soluble domains and the transmembrane domain into models of the full-length membrane protein. Our protocol does not require an interface between the domains and samples possible domain orientations based on backbone dihedrals in the flexible linker regions, created via fragment insertion, while keeping the transmembrane domain fixed in the membrane. Our method, mp_domain_assembly, implemented in RosettaMP samples domain orientations close to the native structure and is best used in conjunction with experimental data to reduce the conformational search space.

scholarly journals Peripheral Myelin Protein 22 Preferentially Partitions into Ordered Phase Membrane Domains

2020 ◽  
Author(s):  
Justin T. Marinko ◽  
Geoffrey C. Li ◽  
Anne K. Kenworthy ◽  
Charles R. Sanders
Keyword(s):  
Membrane Proteins ◽  
Transmembrane Domain ◽  
Transmembrane Proteins ◽  
Cholesterol Homeostasis ◽  
Myelin Protein ◽  
Membrane Domains ◽  
Peripheral Myelin Protein 22 ◽  
Peripheral Myelin Protein ◽  
Disordered Phase ◽  
Phase Preference

AbstractThe ordered environment of membrane rafts is thought to exclude many transmembrane proteins. Nevertheless, some multi-pass transmembrane proteins have been proposed to partition into ordered domains. Here, giant plasma membrane vesicles (GPMVs) were employed to quantitatively show that the tetraspan peripheral myelin protein 22 (PMP22) exhibits a pronounced preference for, promotes the formation of, and stabilizes ordered membrane domains. Neither S-palmitoylation of PMP22 nor its putative cholesterol binding motifs are required for partitioning to ordered domains. In contrast, disruption of its unusual first transmembrane helix (TM1) reduced ordered phase preference. Charcot-Marie-Tooth disease-causing mutations that destabilize PMP22 also reduced or eliminated this preference in favor of the disordered phase. These studies demonstrate PMP22’s ordered phase preference derives both from the distinctive properties of TM1 and global structural features associated with its transmembrane domain, providing a first glimpse at the structural factors that promote raft partitioning for multi-pass proteins.Significance StatementThe preferential partitioning of single span membrane proteins for the ordered phase of ordered/disordered phase-separated membranes is now reasonably well understood, but little is known about this phase preferences of multi-pass membrane proteins. Here, it is shown that the disease-linked tetraspan integral membrane protein, PMP22, displays a pronounced preference to partition into the ordered phase, a preference that is reversed by disease mutations. This phase preference may be related to the role of PMP22 in cholesterol homeostasis in myelinating Schwann cells, a role that is also known to be disrupted under conditions of CMTD peripheral neuropathy caused by pmp22 mutations.

scholarly journals Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics

2018 ◽  
Author(s):  
Alba Torrents de la Peña ◽  
Kimmo Rantalainen ◽  
Christopher A. Cottrell ◽  
Joel D. Allen ◽  
Marit J. van Gils ◽  
...  
Keyword(s):  
Envelope Glycoprotein ◽  
Neutralizing Antibodies ◽  
Transmembrane Domain ◽  
Cytoplasmic Tail ◽  
Full Length ◽  
Broadly Neutralizing Antibodies ◽  
Vaccine Research ◽  
Similarities And Differences ◽  
Membrane Tether ◽  
Hiv 1

AbstractThe HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, such as SOSIP trimers, have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs. We therefore performed a direct and thorough comparison of a full-length native Env trimer containing the transmembrane domain and the cytoplasmic tail, with the sequence matched soluble SOSIP trimer, both based on an early Env sequence (AMC011) from an HIV+ individual that developed bNAbs. The structures of the full-length AMC011 trimer bound to either bNAb PGT145 or PGT151 were very similar to the structures of SOSIP trimers. Antigenically, the full-length and SOSIP trimers were comparable, but in contrast to the full-length trimer, the SOSIP trimer did not bind at all to non-neutralizing antibodies, most likely as a consequence of the intrinsic stabilization of the SOSIP trimer. Furthermore, the glycan composition of full-length and SOSIP trimers was similar overall, but the SOSIP trimer possessed slightly less complex and less extensively processed glycans, which may relate to the intrinsic stabilization as well as the absence of the membrane tether. These data provide insights into how to best use and improve membrane-associated full-length and soluble SOSIP HIV-1 Env trimers as immunogens.

scholarly journals A Survey of Membrane Proteins in Human Serum

2012 ◽  
Vol 5 ◽  
pp. PRI.S9374 ◽  
Author(s):  
Nguyen Tien Dung ◽  
Phan Van Chi
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Human Serum ◽  
Transmembrane Domain ◽  
Tissue Sample ◽  
Ionization Mass ◽  
Post Translational Modifications ◽  
Molecular Weights ◽  
Normal Human ◽  
Nano Liquid Chromatography

Serum and membrane proteins are two of the most attractive targets for proteomic analysis. Previous membrane protein studies tend to focus on tissue sample, while membrane protein studies in serum are still limited. In this study, an analysis of membrane proteins in normal human serum was carried out. Nano-liquid chromatography-electrospray ionization mass spectrometry (NanoLC-ESI-MS/MS) and bioinformatics tools were used to identify membrane proteins. Two hundred and seventeen membrane proteins were detected in the human serum, of which 129 membrane proteins have at least one transmembrane domain (TMD). Further characterizations of identified membrane proteins including their subcellular distributions, molecular weights, post translational modifications, transmembrane domains and average of hydrophobicity, were also implemented. Our results showed the potential of membrane proteins in serum for diagnosis and treatment of diseases.

scholarly journals Plasma Membrane Protein Nce102 Modulates Morphology and Function of the Yeast Vacuole

Biomolecules ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1476
Author(s):  
Katarina Vaskovicova ◽  
Petra Vesela ◽  
Jakub Zahumensky ◽  
Dagmar Folkova ◽  
Maria Balazova ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Vacuolar Membrane ◽  
Yeast Culture ◽  
Membrane Domains ◽  
Biological Functions ◽  
Plasma Membrane Protein ◽  
Cell Architecture ◽  
And Function

Membrane proteins are targeted not only to specific membranes in the cell architecture, but also to distinct lateral microdomains within individual membranes to properly execute their biological functions. Yeast tetraspan protein Nce102 has been shown to migrate between such microdomains within the plasma membrane in response to an acute drop in sphingolipid levels. Combining microscopy and biochemistry methods, we show that upon gradual ageing of a yeast culture, when sphingolipid demand increases, Nce102 migrates from the plasma membrane to the vacuole. Instead of being targeted for degradation it localizes to V-ATPase-poor, i.e., ergosterol-enriched, domains of the vacuolar membrane, analogous to its plasma membrane localization. We discovered that, together with its homologue Fhn1, Nce102 modulates vacuolar morphology, dynamics, and physiology. Specifically, the fusing of vacuoles, accompanying a switch of fermenting yeast culture to respiration, is retarded in the strain missing both proteins. Furthermore, the absence of either causes an enlargement of ergosterol-rich vacuolar membrane domains, while the vacuoles themselves become smaller. Our results clearly show decreased stability of the V-ATPase in the absence of either Nce102 or Fhn1, a possible result of the disruption of normal microdomain morphology of the vacuolar membrane. Therefore, the functionality of the vacuole as a whole might be compromised in these cells.

scholarly journals GBS type III oligosaccharides containing a minimal protective epitope can be turned into effective vaccines by multivalent presentation

2019 ◽  
Author(s):  
F Carboni ◽  
F Angiolini ◽  
M Fabbrini ◽  
B Brogioni ◽  
A Corrado ◽  
...  
Keyword(s):  
Immune Responses ◽  
Group B Streptococcus ◽  
Full Length ◽  
Native Structure ◽  
Protective Response ◽  
Type Iii ◽  
Protective Epitope ◽  
Glycoconjugate Vaccines ◽  
Synthetic Oligosaccharides ◽  
Group B

Abstract Recent structural studies demonstrated that the epitope recognized by a monoclonal antibody representative of the protective response against the type III Group B Streptococcus polysaccharide was comprised within two of the repeating units that constitute the full-length native structure. Here we took advantage of this discovery to design a novel vaccine based on multivalent presentation of the identified minimal epitope on a carrier protein. We show that highly glycosylated short oligosaccharide conjugates elicit functional immune responses comparable to the full-length native polysaccharide. The obtained results pave the way to the design of well-defined glycoconjugate vaccines based on short synthetic oligosaccharides.

scholarly journals Distinct Animal Food Allergens Form IgE-Binding Amyloids

Allergies ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 2
Author(s):  
Raquel Pérez-Tavarez ◽  
Milagros Castellanos ◽  
David Loli-Ausejo ◽  
María Pedrosa ◽  
José Luis Hurtado ◽  
...  
Keyword(s):  
Immunoglobulin E ◽  
Allergic Patient ◽  
Full Length ◽  
Food Allergens ◽  
Native Structure ◽  
Animal Food ◽  
Ige Binding ◽  
D 12

Several animal food allergens assemble into amyloids under gastric-like environments. These aggregated structures provide Gad m 1 with an enhanced immunoglobulin E (IgE) interaction due to the fibrillation of the epitope regions. However, whether these properties are unique to Gad m 1 or shared by other food allergens has not yet been addressed. Using Bos d 5, Bos d 12 and Gal d 2 as allergen models and Gad m 1 as the control, aggregation reactions and the sera of milk, egg and fish allergic patients have been analyzed, assessing the IgE interactions of their amyloids. We found that amyloids formed by Bos d 12 and Gal d 2 full-length and truncated chains are recognized by the IgEs of milk and egg allergic patient sera. As with Gad m 1, in most cases amyloid recognition is higher than that of the native structure. Bos d 5 was not recognized under any fold by the IgE of the sera studied. These results suggest that the formation of IgE-binding amyloids could be a common feature to animal food allergens.

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