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lördag 9 maj 2020

SARS-2 CoV nsp4 proteiinin interaktiot ihmisen proteiinien kanssa. Ainakin 8 interaktioproteiinia.

Tästä SARS-2-CoV nsp4 proteiinista sanotaan että se on transmembraanin ja viruksen replikaatio-transkirptiokompleksin kalvoja muokkaileva ankkuri. Se sovittelee kalvoja toisiinsa ja rekrytoi kalvomateriaa, jotta muosotuu  kiemurtelevaa poimuileva rakennelmaa, jonka poimuista  tuleva virionin valmistelu  saa  turvallisen  kehtonsa, niin ettei  "ympäröivä paha maailma", siis ihmisen  puolustusjärjestelmät  ulotu  syntyvään  uuteen  virursgenomiin.
Nsp4  muodostuu  pitkän replikaasipeptidin aminohappojaksosta  2764-3263  vaivan varhaisimmissa  pilkkoutumisissa  ja on  500 aminohappoa pitkä transmembraanisti (TM) asettuva.

LÄHDE1 antaa tietoa  oletetusta struktuurista ja pääasiallisesta funktiosta.
Swiss model antaa siitä seuraavaa tietoa:
https://swissmodel.expasy.org/repository/species/2697049
Non-structural protein 4 (nsp4): Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles (DMV)  necessary for viral replication.
High quality models are available for the C-terminus which we predict to be a homo-dimer.

Non-structural protein 4
Host membrane
 Multi-pass membrane protein
Host cytoplasm
Localizes in virally-induced cytoplasmic double-membrane vesicles

Non-structural protein 4
Interacts with PL-PRO and nsp6

Plays a role in host membrane rearrangement that leads to creation of cytoplasmic double-membrane vesicles (DMV) necessary for viral replication. Alone appears incapable to induce membrane curvature, but together with nsp3 is able to induce paired membranes. Nsp3, nsp4 and nsp6 together are sufficient to form DMV.1 Publication1 Publication



LÄHDE2  antaa tietoa SARS-2 CoV nsp4 proteiinin interaktioista  isäntäkehon proteiinien kanssa.
löydän listasta seuraavat interaktioproteiinit.
Toiseksi vahvimpia   interaktiokandidaattien   (12 kpl) joukossa on kaksi  nsp4-proteiinin kanssa interaktionsa tekevää, joiden  geenitiedot otan ensiksi  ja asetin  FB- sivulle  8.5. 2020.
Nämä ovat: 
ALG11 (alfa-1,2 mannosyylitransferaasi ),
NUP210  (nukleoporiini210). 

Vähemmän vahvoja interaktioita  tekevien proteiinien suuressa joukossa  (280)  havaitsen seuraavat interaktioproteiinit: niitä katson 9.5. 2020): 
TIMM29, 
TIMM10, 
TIMM9,
TIMM10B.
DNAJC11,
KUVA: https://link.springer.com/article/10.1007/s00441-016-2433-7/figures/1
Lisäksi  mainitaan:
 IDE .


  • TIMM 29 (19p13.2),TIM29, C19orf52.  
 Mitokondrian sisäkalvon translokaasi 29.(https://www.ncbi.nlm.nih.gov/gene/90580 ) Preferred Names: mitochondrial import inner membrane translocase subunit Tim29
Names:  uncharacterized protein C19orf52
uncharacterized conserved protein (DUF2366)
This is a family of proteins conserved from nematodes to humans. The function is not known.


  • IDE,  insuliinia hajoittava tekijä. INSULYSIINI.sinkkimetallopeptidaasi. Hajoittaa bradykiniiniä, kallidiinia, ANP peptidiä.
 Tämä vaikuttaa jokseenkin tehokkaalta peptidaasilta koska verrataan NEP ja ACE- peptidaaseihin, muta tämän sinkkiä sitova kohta  on  käänteisesti rakentunut  (HxxEH).  Sen substraatteja maintiaan  insuliinin ohella  yllättävän paljon: Myös bradykiniini ja kallidiinikin, mikä  kiinnittää huomiotani, vaikka suurin merkitys  näyttää peptidilla olevan  AD- taudin tutkimuksen alueella eikä  immuniteeetin tai tulehduksen kartoilla.  Toinen kohta mikä kiinnitti huomiotani oli vaikutus ANP- peptidiin.

https://www.ncbi.nlm.nih.gov/gene/3416
IDE; insulin degrading Also known as INSULYSIN.
Summary. This gene encodes a zinc metallopeptidase that degrades intracellular insulin, and thereby terminates insulins activity, as well as participating in intercellular peptide signalling by degrading diverse peptides such as glucagon, amylin, bradykinin, and kallidin. The preferential affinity of this enzyme for insulin results in insulin-mediated inhibition of the degradation of other peptides such as beta-amyloid. Deficiencies in this protein's function are associated with Alzheimer's disease and type 2 diabetes mellitus but mutations in this gene have not been shown to be causitive for these diseases. This protein localizes primarily to the cytoplasm but in some cell types localizes to the extracellular space, cell membrane, peroxisome, and mitochondrion. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described but have not been experimentally verified.[provided by RefSeq, Sep 2009 Expression Ubiquitous expression in skin (RPKM 17.4), testis (RPKM 9.9) and 25 other tissues See more Preferred Names: insulin-degrading enzyme
Names: Abeta-degrading protease,
insulin protease,
insulinase.
NP_001159418.1  insulin-degrading enzyme isoform 2.
Conserved Domains (1) summary

Ptr super family cl34066
Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification,
cl25708 Location:2403. Peptidase_M16; Insulinase (Peptidase family M16)
ORIGIN      
        1 msklwfkqdd kfflpkacln feffspfayv dplhcnmayl ylellkdsln eyayaaelag
       61 lsydlqntiy gmylsvkgyn dkqpillkki iekmatfeid ekrfeiikea ymrslnnfra
      121 eqphqhamyy lrllmtevaw tkdelkeald dvtlprlkaf ipqllsrlhi eallhgnitk
      181 qaalgimqmv edtliehaht kpllpsqlvr yrevqlpdrg wfvyqqrnev hnncgieiyy
      241 qtdmqstsen mflelfcqii sepcfntlrt keqlgyivfs gprrangiqg lrfiiqsekp
      301 phylesrvea flitmeksie dmteeafqkh iqalairrld kpkklsaeca kywgeiisqq
      361 ynfdrdntev aylktltked iikfykemla vdaprrhkvs vhvlaremds cpvvgefpcq
      421 ndinlsqapa lpqpeviqnm tefkrglplf plvkphinfm aakl
//

Anthony J. Turner, Natalia N. Nalivaeva, in Handbook of Biologically Active Peptides (Second Edition), 2013  Insulin-Degrading Enzyme (Insulysin, IDE) In addition to insulin, IDE can hydrolyze a number of biologically active peptides including insulin-like growth factor II, tumor growth factor-α, and atrial natriuretic peptide .IDE also degrades somatostatin,
IDE differs from ACE and NEP in possessing an inverted zinc-binding motif 
(His-Xaa-Xaa-Glu-His) and shows unusual allosteric behavior with small peptides.
 


  • TIMM 10, (11q12.1), Mitokondrian sisäkalvon translokaasi 10. 
TIMM10     muodostaa -alfa-propellisen, kuusisiipisen  rakenteen toisen TIM translokaasin , TIM9,   kanssa: Se  toimii   mitokondrian kalvovälitilassa  kaitsijakompleksina liukenemattomille  kuljettaja (carrier) molekyyleille, jotka vievät  mitokondrion tuotteita  mitokondria sisäkalvosuuntaan välikätenä muille  TOM ja TIM komplekseille. (TOM:  tuovat   ulkokalvon läpi)   Tämä kaitsijakompleksi itse on maneettimainen ( jellyfish like) suoja   liukenemattomille kuljettajamolekyyleille.  Ennen kuin TIM9.10 kompleksi muodostuu,  TIM10 ja TIM9  omaavat Zinc finger-  rakenteen,  mutta  kun chaperone (kaitsija)kompleksi on muodostunut, siinä ei ole enää sinkkiä,  vaan  niiden sijasta disulfidisiltoja, jotka eivät redusoidu.   (TIM9•10 has previously undescribed α-propeller architecture with approximate C3 molecular symmetry (Figure 3A).)

  https://www.ncbi.nlm.nih.gov/gene/26519, 
translocase of inner mitochondrial membrane 10. Also known as TIM10; TIM10A; TIMM10A
The mitochondrial protein encoded by this gene belongs to a family of evolutionarily conserved proteins that are organized in heterooligomeric complexes in the mitochondrial intermembrane space. These proteins mediate the import and insertion of hydrophobic membrane proteins into the mitochondrial inner membrane, functioning as intermembrane space chaperones for the highly insoluble carrier proteins 

NP_036588.1  mitochondrial import inner membrane translocase subunit Tim10.
Tim10/DDP family zinc finger: Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein TIMM8A. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localized to the mitochondrial intermembrane space.
(Obs: Positional proteomics analysis identifies the cleavage of human translocase of inner mitochondrial membrane 10 homolog (yeast) (TIMM10) at amino acid residues 72-73 by the HIV-1 protease) .
 CHAPERONE  hexamer TIM9.10 :   DOI:https://doi.org/10.1016/j.molcel.2005.11.010).  Import of proteins into mitochondria occurs by coordinated actions of preprotein translocases in the outer and inner membranes (TOM). Tim9 and Tim10 are translocase components of the intermembrane space, related to deafness-dystonia peptide 1 (DDP1). They coassemble into a hexamer, TIM9•10, which captures and chaperones precursors of inner membrane metabolite carriers as they exit the TOM channel in the outer membrane. The crystal structure of TIM9•10 reveals a previously undescribed α-propeller topology in which helical “blades” radiate from a narrow central pore lined with polar residues. The propeller blades are reminiscent of “tentacles” in chaperones Skp and prefoldin. In each TIM9•10 subunit, a signature “twin CX3C” motif forms two intramolecular disulfides. There is no obvious binding pocket for precursors, which we suggest employ the chaperone-like tentacles of TIM9•10 as surrogate lipid contacts. The first reported crystal structure of a mitochondrial translocase assembly provides insights into selectivity and regulation of precursor import.
  • DNAJC11, (1p36.31), Hsp40-perheen jäsen.
DnaJ Hs40 proteiiniperheen  jäsen C11  on chaperone-molekyylin tapainen ja kuuluu kompleksiin, joka  pitää yllä mitokondriassa morfologiaa ja  membraanien välistä,  funktionaalisesti aivan olennaista toimintatilaa.   (Aromaattiset aminohapot F,Y     antavat tietyn melodian   musiikkiin) https://www.youtube.com/watch?v=LRZLDVXoIoM .

https://www.ncbi.nlm.nih.gov/gene/55735. DNAJC11p.
DnaJ heat shock protein family (Hsp40) member C11.
Also known as dJ126A5.1. Expression Ubiquitous expression in kidney (RPKM 23.0), colon (RPKM 15.3) and 25 other tissues See more
FEATURES:  https://www.ncbi.nlm.nih.gov/protein/NP_060668.2
Evolution and structural organization of the mitochondrial contact
            site (MICOS) complex and the mitochondrial intermembrane space
            bridging (MIB) complex
  NP_060668.2  dnaJ homolog subfamily C member 11
 Conserved Domains (2) summary 
pfam00226 Location:1479 DnaJ; DnaJ domain. DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature.
pfam11875 Location:417549
Domain of unknown function (DUF3395)
This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 147 to 176 amino acids in length. This domain is found associated with pfam00226. https://febs.onlinelibrary.wiley.com/doi/full/10.1016/j.febslet.2007.06.052
https://www.ncbi.nlm.nih.gov/pubmed/17624330/

  • TIMM 10B , (11q15.4)  Mitokondrian sisäkalvon translokaasi 10B.
https://www.ncbi.nlm.nih.gov/gene/26515
translocase of inner mitochondrial membrane 10B. Also known as FXC1; Tim9b; TIM10B
Summary: FXC1, or TIMM10B, belongs to a family of evolutionarily conserved proteins that are organized in heterooligomeric complexes in the mitochondrial intermembrane space. These proteins mediate the import and insertion of hydrophobic membrane proteins into the mitochondrial inner membrane.[supplied by OMIM, Apr 2004] Expression Ubiquitous expression in thyroid (RPKM 18.0), prostate (RPKM 12.0) and 25 other tissues See more.
 Preferred Names: mitochondrial import inner membrane translocase subunit Tim10 B.
Names:fracture callus 1 homolog, fracture callus protein 1,(FXC1),
mitochondrial import inner membrane translocase subunit Tim9 B,
translocase of inner mitochondrial membrane 10 homolog B. 
 FEATURE: https://www.ncbi.nlm.nih.gov/protein/NP_036324.1.
 12..67 /region_name="zf-Tim10_DDP
  Region          28..52 /region_name="Twin CX3C motif". 

  • TIMM 9, (14q23.1) Mitokondrian sisäkalvon translokaasi 9. 
 https://www.ncbi.nlm.nih.gov/gene/26520
Translocase of inner mitochondrial membrane 9. Also known as TIM9; TIM9A.
Summary: TIMM9 belongs to a family of evolutionarily conserved proteins that are organized in heterooligomeric complexes in the mitochondrial intermembrane space. These proteins mediate the import and insertion of hydrophobic membrane proteins into the mitochondrial inner membrane.[supplied by OMIM, Apr 2004]. Expression Ubiquitous expression in thyroid (RPKM 11.9), ovary (RPKM 11.7) and 25 other tissues See more.
Preferred Names: mitochondrial import inner membrane translocase subunit Tim9
Names: translocase of inner mitochondrial membrane 9 homolog. 

 https://www.ncbi.nlm.nih.gov/pubmed/30445040
2018 Nov 15;175(5):1365-1379.e25. doi: 10.1016/j.cell.2018.10.039. Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.
Weinhäupl K1, Lindau C2 The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane (TOM)   and α-helical carrier proteins in the inner membrane (TIM)
The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial "transfer-chaperone" system is able to guide α-helical and β-barrel membrane proteins in a "nascent chain-like" conformation through a ribosome-free compartment.
https://www.researchgate.net/profile/Richard_Wagner2/publication/5674953/figure/fig1/AS:267529880862721@1440795502022/Two-main-protein-import-pathways-of-mitochondria-Presequences-direct-proteins-through.png ---------------


 N-glykaanin biosynteesikartta näyttää ALG11 entsyymin tärkeän sijaintikohdan näiden glykaani   rakenteiden   synteesiketjussa.  Alempi linkki näyttää näitä  synteesirrakenelmia kuin "hirvensarvien" muodostusta. Senkaltaisia  sitten lähetetään proteiinien pintaan ja ne muodostavat  soluja  suojaavia  telinerakenteita:  solujen  Glycocalix.
https://www.genome.jp/kegg-bin/show_pathway?hsa00510
https://www.researchgate.net/figure/Comparison-of-protein-N-glycosylation-pathways-in-eukaryotes-Biosynthesis-steps_fig1_326041354

  • ALG11 (13q14.3)    ( isäntäsolun  glycocalyx-suojakerroksen  synteesin  alkuvaiheen entsyymeitä)
https://www.ncbi.nlm.nih.gov/gene/440138
Official Full Name ALG11 alpha-1,2-mannosyltransferase
Also known as GT8; CDG1P
Summary: This gene encodes a GDP-Man:Man3GlcNAc2-PP-dolichol-alpha1,2-mannosyltransferase which is localized to the cytosolic side of the endoplasmic reticulum (ER) and catalyzes the transfer of the fourth and fifth mannose residue from GDP-mannose (GDP-Man) to Man3GlcNAc2-PP-dolichol and Man4GlcNAc2-PP-dolichol resulting in the production of Man5GlcNAc2-PP-dolichol. Mutations in this gene are associated with congenital disorder of glycosylation type Ip (CDGIP). This gene overlaps but is distinct from the UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast) gene. A pseudogene of the GDP-Man:Man3GlcNAc2-PP-dolichol-alpha1,2-mannosyltransferase has been identified on chromosome 19. [provided by RefSeq, Aug 2010] Expression Ubiquitous expression in thyroid (RPKM 12.1), kidney (RPKM 8.8) and 25 other tissues
Preferred Names
GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
Names
GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase
asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog
asparagine-linked glycosylation protein 11 homolog
glycolipid 2-alpha-mannosyltransferase.
FEATURES:
  1. NM_001004127.3NP_001004127.2  GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase
    Conserved Domains (1) summary

    cd03806
    Location:63480
    GT1_ALG11_like; This family is most closely related to the GT1 family of glycosyltransferases. ALG11 in yeast is involved in adding the final 1,2-linked Man to the Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of the ER. The deletion analysis of ALG11 was shown to block the early steps of core biosynthesis that takes place on the cytoplasmic face of the ER and lead to a defect in the assembly of lipid-linked oligosaccharides.
Siis virusinteraktio voi vahingoittaa   isäntäsolujen glycocalixsuojakerroksen.
https://ccforum.biomedcentral.com/articles/10.1186/s13054-018-2292-6

  •  NUP210 (3p25.1) , ( nukleoporiini 210).

https://www.ncbi.nlm.nih.gov/gene/23225
Official Full Name  nucleoporin 210.
Also known as GP210; POM210.
Summary. The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a membrane-spanning glycoprotein (gp)  that is a major component of the nuclear pore complex. Multiple pseudogenes related to this gene are located on chromosome 3. [provided by RefSeq, Jul 2013] Expression Broad expression in lymph node (RPKM 17.2), bone marrow (RPKM 15.9) and 22 other tissues .
Preferred Names  nuclear pore membrane glycoprotein 210
Names: 
nuclear envelope pore membrane protein POM 210,
nuclear pore protein gp210,
nucleoporin 210kDa,
nucleoporin Nup210,
pore membrane protein of 210 kDa. 
 FEATURES: 
NP_079199.2  nuclear pore membrane glycoprotein 210 precursor 
Conserved Domains (1) summary
Ig-like domain-containing protein (domain architecture ID 10492496)
bacterial Ig-like domain-containing protein similar to human nuclear pore membrane glycoprotein 210 and Escherichia virus T5 major tail tube protein pb6
pfam02368
Location:10791152
Big_2; Bacterial Ig-like domain (group 2) This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial and phage surface proteins such as intimins.
Mitä nämä NUP- geenit ovat?  
Nukleoporiinin tehtävä on estää suurten proteiinien diffuusiota tuman ja soluliman välillä.

 Nukleoporiineja on   kymmenä geenituotteita Ne toimivat kymmenien proteiinien yhteistyöllä  kompleksina muodostamassa sitä aukkoa,  josta tapahtuu nukleosytoplasminen kuljetus.
SARS-2-CoV nsp 9 tekee interaktion NUP88 , NUP62. NUP58, NUP214, NUP54 ja
SARS.2-CoV ORF6 tekee interaktion NUP98 kanssa. Lueteltu interaktiovahvuuden mukaisessa järjestyksessä. 
kovasti näyttää  Sars-2- viruksella olevan kiinnosusta tähän sytosolin ja tuman väliseen porttiin ja  materian  kuljetukseen.

 Tieto nukleoporiineista vuonna 2002:
 https://www.ncbi.nlm.nih.gov/pubmed/12196509?dopt=Abstract
2002 Sep 2;158(5):915-27. Epub 2002 Aug 26.
Proteomic analysis of the mammalian nuclear pore complex.
Abstract
As the sole site of nucleocytoplasmic transport, the nuclear pore complex (NPC) has a vital cellular role. Nonetheless, much remains to be learned about many fundamental aspects of NPC function. To further understand the structure and function of the mammalian NPC, we have completed a proteomic analysis to identify and classify all of its protein components. We used mass spectrometry to identify all proteins present in a biochemically purified NPC fraction. Based on previous characterization, sequence homology, and subcellular localization, 29 of these proteins were classified as nucleoporins, and a further 18 were classified as NPC-associated proteins. Among the 29 nucleoporins were six previously undiscovered nucleoporins and a novel family of WD repeat nucleoporins. One of these WD repeat nucleoporins is ALADIN, the gene mutated in triple-A (or Allgrove) syndrome. Our analysis defines the proteome of the mammalian NPC for the first time and paves the way for a more detailed characterization of NPC structure and functionValaiseva kuva vuodelta 2012
https://www.annualreviews.org/na101/home/literatum/publisher/ar/journals/content/biophys/2012/biophys.2012.41.issue-1/annurev-biophys-050511-102328/production/images/medium/bb410557.f2.gif

Muistiin  aluksi   tietoa kahdesta melko vahvasta interaktioproteiinista ALG11 ja NUP210.
Varsinaiset nukleaariseen kuljetukseen sekaantuvat virusproteiinit ovat nsp9, nsp15 ja ORF6, vaikka  nsp 4 myös osallistuu. Varsinaisesti  nsp4 vaikuttaa mitokondriassa.  Niistä interaktioproteiineista myöhemmin.  myöhemmin.

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