Summary: Negative factor, (F-Protein) or Nef
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Nef (protein) Edit Wikipedia article
|Negative factor, (F-Protein) or Nef|
Nef (Negative Regulatory Factor) is a small 27-35 kDa myristoylated protein encoded by primate lentiviruses. These include Human Immunodeficiency Viruses (HIV-1 and HIV-2) and Simian Immunodeficiency Virus (SIV). Nef localizes primarily to the cytoplasm but also partially to the Plasma Membrane (PM) and is one of many pathogen-expressed proteins, known as virulence factors, which function to manipulate the host's cellular machinery and thus allow infection, survival or replication of the pathogen. Nef stands for "Negative Factor" and although it is often considered dispensable for HIV-1 replication, in infected hosts the viral protein markedly elevates viral titers. 
The expression of Nef early in the viral life cycle ensures T-cell activation and the establishment of a persistent state of infection, two basic attributes of HIV infection. Viral expression of Nef induces numerous changes within the infected cell including the modulation of protein cell surface expression, cytoskeletal remodeling, and signal transduction. Since the activation state of the infected cell plays an important role in the success rate of HIV-1 infection, it is important that resting T-cells be primed to respond to T-cell receptor (TCR) stimuli. HIV-1 Nef lowers the threshold for activation of CD4+ lymphocytes, but is not sufficient to cause activation in the absence of exogenous stimuli.
By down regulating cell surface expression of CD4 and Lck, Nef creates a narrow TCR response which likely optimizes HIV-1 viral production and generates a susceptible population of cells to further infect. Nef retargets kinase-active Lck away from the plasma membrane to early and recycling endosomes (RE) as well as the Trans-Golgi network (TGN). RE/TGN associated Lck sub-populations in Nef expressing cells are in the catalytically active conformation and thus signaling competent. While TCR signaling takes place at the plasma membrane (PM), activation of the Ras-GTPase takes place in intracellular compartments including the Golgi apparatus. Nef induced enrichment of active Lck in these compartments results in an increase of localized RAS activity and enhanced activation of Erk kinase and the production of Interleukin-2 (IL-2). Since IL-2 is known to activate the growth, proliferation, and differentiation of T-cells to become effector T-cells this is a self-serving effect that creates a new population of cells in which HIV-1 is able to infect. Self-activation of the infected cell by IL-2 also stimulates the cell to become an effector cell and initiate the machinery which HIV-1 relies upon for its own proliferation.
To further evade the host immune response, Nef down-regulates the cell surface and total expression of the negative immune modulator CTLA-4 by targeting the protein for lysosomal degradation. In contrast to CD28 which activates T-cells, CTLA-4 is essentially an “off-switch” which would inhibit the viral production if it were activated. Lentiviruses such as HIV-1 have acquired proteins such as Nef which perform a wide array of functions including the identification of CTLA-4 before it reaches the PM and tagging it for degradation. Nef is also known to phosphorylate and inactivate Bad, a proapoptotic member of the Bcl-2 family thus protecting the infected cells from apoptosis.
Cytoskeletal remodeling is thought to reduce TCR signaling during early infection and is also modulated to some degree by Nef. Actin remodeling is generally modulated by the actin severing factor cofilin. Nef is able to associate with the cellular kinase PAK2 which phosphorylates and inactivates cofilin and interferes with early TCR signaling.
One group of patients in Sydney were infected with a nef-deleted virus and took much longer than expected to progress to AIDS.
- Das SR, Jameel S (April 2005). "Biology of the HIV Nef protein". Indian J. Med. Res. 121 (4): 315–32. PMID 15817946.
- Marcey D, Somple M, Silva N (2007-01-01). "HIV-1 Nef Protein". The Online Macromolecular Museum Exhibits. California Lutheran University. Retrieved 2008-08-06.
- Abraham L, Fackler OT (December 2012). "HIV-1 Nef: a multifaceted modulator of T cell receptor signaling". Cell Communication and Signaling 10 (1): 39. doi:10.1186/1478-811X-10-3. PMID 23227982.
- Laguette N, Bregnard C, Benichou S, Basmaciogullari S (June 2010). "Human immunodeficiency virus (HIV) type-1, HIV-2 and simian immunodeficiency virus Nef proteins.". Mol. Aspects Med. 31 (5): 418–33. doi:10.1016/j.mam.2010.05.003. PMID 20594957.
- Geyer M, Fackler OT, Peterlin BM (July 2001). "Structure–function relationships in HIV-1 Nef". EMBO 2 (7): 580–5. doi:10.1093/embo-reports/kve141. PMC 1083955. PMID 11463741.
- El-Far M, Isabelle C, Chomont N, Bourbonnière M, Fonseca S, Ancuta P, Peretz Y, Chouikh Y, Halwani R, Schwartz O, Madrenas J, Freeman GJ, Routy JP, Haddad EK, Sékaly RP. (January 2013). "Down-Regulation of CTLA-4 by HIV-1 Nef Protein". PLoS ONE 8 (1): e54295. doi:10.1371/journal.pone.0054295. PMID 23372701.
- Learmont JC, Geczy AF, Mills J, Ashton LJ, Raynes-Greenow CH, Garsia RJ, Dyer WB, McIntyre L, Oelrichs RB, Rhodes DI, Deacon NJ, Sullivan JS' (June 1999). "Immunologic and virologic status after 14 to 18 years of infection with an attenuated strain of HIV-1. A report from the Sydney Blood Bank Cohort". N. Engl. J. Med. 340 (22): 1715–22. doi:10.1056/NEJM199906033402203. PMID 10352163.
- Daniel MD, Kirchhoff F, Czajak SC, Sehgal PK, Desrosiers RC (December 1992). "Protective effects of a live attenuated SIV vaccine with a deletion in the nef gene". Science 258 (5090): 1938–41. doi:10.1126/science.1470917. PMID 1470917.
- Muthumani K, Choo AY, Hwang DS, Premkumar A, Dayes NS, Harris C, Green DR, Wadsworth SA, Siekierka JJ, Weiner DB (September 2005). "HIV-1 Nef-induced FasL induction and bystander killing requires p38 MAPK activation". Blood 106 (6): 2059–68. doi:10.1182/blood-2005-03-0932. PMC 1895138. PMID 15928037.
- Piguet V, Trono D (1999). "The Nef protein of primate lentiviruses". Rev. Med. Virol. 9 (2): 111–20. doi:10.1002/(SICI)1099-1654(199904/06)9:2<111::AID-RMV245>3.0.CO;2-P. PMID 10386338.
- Janardhan A, Swigut T, Hill B et al. (January 2004). "HIV-1 Nef Binds the DOCK2–ELMO1 Complex to Activate Rac and Inhibit Lymphocyte Chemotaxis". PLoS Biol. 2 (1): e6. doi:10.1371/journal.pbio.0020006. PMC 314466. PMID 14737186.
- Michael Smith. "HIV protein hides infected cells from immune system". MedPageToday.com. Retrieved 2008-09-26.
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Negative factor, (F-Protein) or Nef Provide feedback
Nef protein accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src kinase family.
Arold S, Franken P, Strub M-P, Hoh F, Benichou S, Benarous R, Dumas C; , Structure 1997;5:1361-1372.: The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signalling PUBMED:9351809 EPMC:9351809
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001558
Human immunodeficiency virus 1 (HIV-1) negative factor (Nef protein) accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases [PUBMED:9351809].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||GTP binding (GO:0005525)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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Gladomain, followed by two consecutive
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_128 (release 1.0)|
|Number in seed:||20|
|Number in full:||19129|
|Average length of the domain:||175.30 aa|
|Average identity of full alignment:||58 %|
|Average coverage of the sequence by the domain:||97.39 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the F-protein domain has been found. There are 35 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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