Major intrinsic proteins

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Major intrinsic protein
PDB 1fx8 EBI.jpg
Structure of a glycerol-conducting channel. [1]
Identifiers
SymbolMIP
Pfam PF00230
InterPro IPR000425
PROSITE PDOC00193
SCOP2 1fx8 / SCOPe / SUPFAM
TCDB 1.A.8
OPM superfamily 7
OPM protein 1z98
CDD cd00333
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

Major intrinsic proteins comprise a large superfamily of transmembrane protein channels that are grouped together on the basis of homology. The MIP superfamily includes three subfamilies: aquaporins, aquaglyceroporins and S-aquaporins. [2]

Contents

  1. The aquaporins (AQPs) are water selective.
  2. The aquaglyceroporins are permeable to water, but also to other small uncharged molecules such as glycerol.
  3. The third subfamily, with little conserved amino acid sequences around the NPA boxes, include 'superaquaporins' (S-aquaporins).

The phylogeny of insect MIP family channels has been published. [3] [4] [5]

Families

There are two families that belong to the MIP Superfamily.

The Major Intrinsic Protein Family (TC# 1.A.8)

The MIP family is large and diverse, possessing thousands of members that form transmembrane channels. These channel proteins function in transporting water, small carbohydrates (e.g., glycerol), urea, NH3, CO2, H2O2 and ions by energy-independent mechanisms. For example, the glycerol channel, FPS1p of Saccharomyces cerevisiae mediates uptake of arsenite and antimonite. [6] Ion permeability appears to occur through a pathway different than that used for water/glycerol transport and may involve a channel at the 4 subunit interface rather than the channels through the subunits. [7] MIP family members are found ubiquitously in bacteria, archaea and eukaryotes. Phylogenetic clustering of the proteins is primarily based according to phylum of the organisms of origin, but one or more clusters are observed for each phylogenetic kingdom (plants, animals, yeast, bacteria and archaea). [8] MIPs are classified into five subfamilies in higher plants, including plasma membrane (PIPs), tonoplast (TIPs), NOD26-like (NIPs), small basic (SIPs) and unclassified X (XIPs) intrinsic proteins. One of the plant clusters includes only tonoplast (TIP) proteins, while another includes plasma membrane (PIP) proteins. [9]

Major Intrinsic Protein

The Major Intrinsic Protein (MIP) of the human lens of the eye (Aqp0), after which the MIP family was named, represents about 60% of the protein in the lens cell. In the native form, it is an aquaporin (AQP), but during lens development, it becomes proteolytically truncated. The channel, which normally houses 6-9 water molecules, becomes constricted so only three remain, and these are trapped in a closed conformation. [10] [11] These truncated tetramers form intercellular adhesive junctions (head to head), yielding a crystalline array that mediates lens formation with cells tightly packed as required to form a clear lens. [12] Lipids crystallize with the protein. [13] Ion channel activity has been shown for Aquaporins 0, 1, and 6, Drosophila 'Big Brain' (bib) [14] and plant Nodulin-26. [15] Roles of aquaporins in human cancer have been reviewed as have their folding pathways. [16] [17] AQPs may act as transmembrane osmosensors in red cells, secretory granules and microorganisms. [18] MIP superfamily proteins and variations of their selectivity filters have been reviewed. [19]

Aquaporin

The currently known aquaporins cluster loosely together as do the known glycerol facilitators. [20] MIP family proteins are believed to form aqueous pores that selectively allow passive transport of their solute(s) across the membrane with minimal apparent recognition. Aquaporins selectively transport glycerol as well as water while glycerol facilitators selectively transport glycerol but not water. Some aquaporins can transport NH3 and CO2. Glycerol facilitators function as solute nonspecific channels, and may transport glycerol, dihydroxyacetone, propanediol, urea and other small neutral molecules in physiologically important processes. Some members of the family, including the yeast Fps1 protein (TC# 1.A.8.5.1) and tobacco NtTIPa (TC# 1.A.8.10.2) may transport both water and small solutes. [20]

Examples

A list of nearly 100 currently classified members of the MIP family can be found in the Transporter Classification Database. Some of the MIP family channels include:

  • Mammalian major intrinsic protein (MIP). MIP is the major component of lens fibre gap junctions.
  • Mammalian aquaporins. [20] (InterPro :  IPR012269 ) These proteins form water-specific channels that provide the plasma membranes of red cells, as well as kidney proximal and collecting tubules with high permeability to water, thereby permitting water to move in the direction of an osmotic gradient.
  • Soybean nodulin-26, a major component of the peribacteroid membrane induced during nodulation in legume roots after Rhizobium infection.
  • Plant tonoplast intrinsic proteins (TIP). There are various isoforms of TIP : alpha (seed), gamma, Rt (root), and Wsi (water-stress induced). These proteins may allow the diffusion of water, amino acids and/or peptides from the tonoplast interior to the cytoplasm.
  • Bacterial glycerol facilitator protein (gene glpF), which facilitates the movement of glycerol non-specifically across the cytoplasmic membrane. [21]
  • Salmonella typhimurium propanediol diffusion facilitator (gene pduF).
  • Yeast FPS1, a glycerol uptake/efflux facilitator protein.
  • Drosophila neurogenic protein 'big brain' (bib). This protein may mediate intercellular communication; it may functions by allowing the transport of certain molecules(s) and thereby sending a signal for an exodermal cell to become an epidermoblast instead of a neuroblast.
  • Yeast hypothetical protein YFL054c.
  • A hypothetical protein from the pepX region of Lactococcus lactis .

Structure

MIP family channels consist of homotetramers (e.g., GlpF of E. coli; TC #1.A.8.1.1, AqpZ of E. coli; TC #1.A.8.3.1, and MIP or Aqp0 of Bos taurus; TC #1.A.8.8.1). Each subunit spans the membrane six times as putative α-helices. The 6 TMS domains are believed to have arisen from a 3-spanner-encoding genetic element by a tandem, intragenic duplication event. The two halves of the proteins are therefore of opposite orientation in the membrane. A well-conserved region between TMSs 2 and 3 and TMSs 5 and 6 dip into the membrane, each loop forming a half TMS. [22] [23] A common amino acyl motif in these transporters is an asparagine–proline–alanine (NPA) motif. Aquaporins generally have the NPA motif in both halves, the glycerol facilitators generally have an NPA motif in the first haves and a DPA motif in the second halves, and the super-aquaporins have poorly conserved NPA motifs in both halves. [2]

Glycerol Uptake Facilitator

The crystal structure of the glycerol facilitator of E. coli (TC# 1.A.8.1.1) was solved at 2.2 Å resolution ( PDB: 1FX8 ​). [24] Glycerol molecules create a single file within the channel and pass through a narrow selectivity filter. The two conserved D-P-A motifs in the loops between TMSs 2 and 3 and TMSs 5 and 6 form the interface between the two duplicated halves of each subunit. Thus each half of the protein forms 3.5 TMSs surrounding the channel. The structure explains why GlpF is selectively permeable to straight chain carbohydrates, and why water and ions are largely excluded. Aquaporin-1 (AQP1) and the bacterial glycerol facilitator, GlpF can transport O2, CO2, NH3, glycerol, urea, and water to varying degrees. For small solutes passing through AQP1, there is an anti-correlation between permeability and solute hydrophobicity. [25] AQP1 is thus a selective filter for small polar solutes, whereas GlpF is highly permeable to small solutes and less permeable to larger solutes.

Aquaporin-1

Aquaporin-1 (Aqp1) from the human red blood cell has been solved by electron crystallography to 3.8 Å resolution ( PDB: 1FQY ​). [26] The aqueous pathway is lined with conserved hydrophobic residues that permit rapid water transport. Water selectivity is due to a constriction of the inner pore diameter to about 3 Å over the span of a single residue, superficially similar to that in the glycerol facilitator of E. coli. Several other more recently resolved crystal structures are available in RCSB, including but not limited to: PDB: 4CSK ​, 1H6I ​, 1IH5 ​.

Aquaporin-Z

AqpZ, a homotetramer (tAqpZ) of four water-conducting channels that facilitate rapid water movements across the plasma membrane of E. coli, has been solved to 3.2 Å resolution ( PDB: 2ABM ​). All channel-lining residues in the four monomeric channels are orientated in nearly identical positions except at the narrowest channel constriction, where the side chain of a conserved Arg-189 adopts two distinct orientations. In one of the four monomers, the guanidino group of Arg-189 points toward the periplasmic vestibule, opening up the constriction to accommodate the binding of a water molecule through a tridentate H-bond. In the other three monomers, the Arg-189 guanidino group bends over to form an H-bond with carbonyl oxygen of Thr-183 occluding the channel. Therefore, the tAqpZ structure has two different Arg-189 conformations which provide water permeation through the channel. Alternating between the two Arg-189 conformations disrupts continuous flow of water, thus regulating the open probability of the water pore. Further, the difference in Arg-189 displacements is correlated with a strong electron density found between the first transmembrane helices of two open channels, suggesting that the observed Arg-189 conformations are stabilized by asymmetrical subunit interactions in tAqpZ. [27] Other resolved crystal structures for AqpZ include: PDB: 3NK5 ​, 3NKC ​, 1RC2 ​.

PIP1 and PIP2

The 3-D structures of the open and closed forms of plant aquaporins, PIP1 and PIP2, have been solved ( PDB: 4JC6 ​). In the closed conformation, loop D caps the channel from the cytoplasm and thereby occludes the pore. In the open conformation, loop D is displaced up to 16 Å, and this movement opens a hydrophobic gate blocking the channel entrance from the cytoplasm. These results reveal a molecular gating mechanism which appears conserved throughout all plant plasma membrane aquaporins. In plants it regulates water intake/export in response to water availability and cytoplasmic pH during anoxia. [28]

Human proteins containing this domain

AQP1, AQP2, AQP3, AQP4, AQP5, AQP6 , AQP7, AQP8, AQP9, AQP10 , MIP

See also

Related Research Articles

<span class="mw-page-title-main">Semipermeable membrane</span> Membrane which will allow certain molecules or ions to pass through it by diffusion

Semipermeable membrane is a type of biological or synthetic, polymeric membrane that will allow certain molecules or ions to pass through it by osmosis. The rate of passage depends on the pressure, concentration, and temperature of the molecules or solutes on either side, as well as the permeability of the membrane to each solute. Depending on the membrane and the solute, permeability may depend on solute size, solubility, properties, or chemistry. How the membrane is constructed to be selective in its permeability will determine the rate and the permeability. Many natural and synthetic materials which are rather thick are also semipermeable. One example of this is the thin film on the inside of the egg.

<span class="mw-page-title-main">Aquaporin</span> Cellular membrane structure that selectively passes water

Aquaporins, also called water channels, are channel proteins from a larger family of major intrinsic proteins that form pores in the membrane of biological cells, mainly facilitating transport of water between cells. The cell membranes of a variety of different bacteria, fungi, animal and plant cells contain aquaporins through which water can flow more rapidly into and out of the cell than by diffusing through the phospholipid bilayer. Aquaporins have six membrane-spanning alpha helical domains with both carboxylic and amino terminals on the cytoplasmic side. Two hydrophobic loops contain conserved asparagine-proline-alanine which form a barrel surrounding a central pore-like region that contains additional protein density. Because aquaporins are usually always open and are prevalent in just about every cell type, this leads to a misconception that water readily passes through the cell membrane down its concentration gradient. Water can pass through the cell membrane through simple diffusion because it is a small molecule, and through osmosis, in cases where the concentration of water outside of the cell is greater than that of the inside. However, because water is a polar molecule this process of simple diffusion is relatively slow, and in tissues with high water permeability the majority of water passes through aquaporin.

<span class="mw-page-title-main">Passive transport</span> Transport that does not require energy

Passive transport is a type of membrane transport that does not require energy to move substances across cell membranes. Instead of using cellular energy, like active transport, passive transport relies on the second law of thermodynamics to drive the movement of substances across cell membranes. Fundamentally, substances follow Fick's first law, and move from an area of high concentration to one of low concentration because this movement increases the entropy of the overall system. The rate of passive transport depends on the permeability of the cell membrane, which, in turn, depends on the organization and characteristics of the membrane lipids and proteins. The four main kinds of passive transport are simple diffusion, facilitated diffusion, filtration, and/or osmosis.

A membrane transport protein is a membrane protein involved in the movement of ions, small molecules, and macromolecules, such as another protein, across a biological membrane. Transport proteins are integral transmembrane proteins; that is they exist permanently within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion or active transport. The two main types of proteins involved in such transport are broadly categorized as either channels or carriers. The solute carriers and atypical SLCs are secondary active or facilitative transporters in humans. Collectively membrane transporters and channels are known as the transportome. Transportomes govern cellular influx and efflux of not only ions and nutrients but drugs as well.

<span class="mw-page-title-main">Aquaporin-4</span> Protein-coding gene in the species Homo sapiens

Aquaporin-4, also known as AQP-4, is a water channel protein encoded by the AQP4 gene in humans. AQP-4 belongs to the aquaporin family of integral membrane proteins that conduct water through the cell membrane. A limited number of aquaporins are found within the central nervous system (CNS): AQP1, 3, 4, 5, 8, 9, and 11, but more exclusive representation of AQP1, 4, and 9 are found in the brain and spinal cord. AQP4 shows the largest presence in the cerebellum and spinal cord grey matter. In the CNS, AQP4 is the most prevalent aquaporin channel, specifically located at the perimicrovessel astrocyte foot processes, glia limitans, and ependyma. In addition, this channel is commonly found facilitating water movement near cerebrospinal fluid and vasculature.

<span class="mw-page-title-main">Aquaporin-2</span> Protein-coding gene in the species Homo sapiens

Aquaporin-2 (AQP-2) is found in the apical cell membranes of the kidney's collecting duct principal cells and in intracellular vesicles located throughout the cell. It is encoded by the AQP2 gene.

<span class="mw-page-title-main">Aquaporin-3</span> Protein-coding gene in the species Homo sapiens

Aquaporin 3 (AQP-3) is the protein product of the human AQP3 gene. It is found in the basolateral cell membrane of principal collecting duct cells and provides a pathway for water to exit these cells. Aquaporin-3 is also permeable to glycerol, ammonia, urea, and hydrogen peroxide. It is expressed in various tissues including the skin, respiratory tract, and kidneys as well as various types of cancers. In the kidney, aquaproin-3 is unresponsive to the antidiuretic hormone vasopressin, unlike aquaporin-2. This protein is also a determinant for the GIL blood group system.

<span class="mw-page-title-main">Aquaporin-1</span> Protein-coding gene in the species Homo sapiens

Aquaporin 1 (AQP-1) is a protein that in humans is encoded by the AQP1 gene.

<span class="mw-page-title-main">Lens fiber major intrinsic protein</span>

Lens fiber major intrinsic protein also known as aquaporin-0 is a protein that in humans is encoded by the MIP gene.

<span class="mw-page-title-main">Aquaporin-5</span> Protein-coding gene in the species Homo sapiens

Aquaporin-5 (AQP-5) is a protein that in humans is encoded by the AQP5 gene.

<span class="mw-page-title-main">Aquaporin-9</span> Protein-coding gene in the species Homo sapiens

Aquaporin-9 (AQP-9) is a protein that in humans is encoded by the AQP9 gene.

<span class="mw-page-title-main">Aquaporin-8</span> Protein-coding gene in the species Homo sapiens

Aquaporin-8 is a protein that in humans is encoded by the AQP8 gene.

<span class="mw-page-title-main">Aquaporin-7</span> Protein-coding gene in the species Homo sapiens

Aquaporin-7 (AQP-7) is a protein that in humans is encoded by the AQP7 gene.

<span class="mw-page-title-main">Intestinal epithelium</span> Single-cell layer lining the intestines

The intestinal epithelium is the single cell layer that form the luminal surface (lining) of both the small and large intestine (colon) of the gastrointestinal tract. Composed of simple columnar epithelial cells, it serves two main functions: absorbing useful substances into the body and restricting the entry of harmful substances. As part of its protective role, the intestinal epithelium forms an important component of the intestinal mucosal barrier. Certain diseases and conditions are caused by functional defects in the intestinal epithelium. On the other hand, various diseases and conditions can lead to its dysfunction which, in turn, can lead to further complications.

<span class="mw-page-title-main">Sodium-solute symporter</span> Group of transport proteins

Members of the Solute:Sodium Symporter (SSS) Family (TC# 2.A.21) catalyze solute:Na+ symport. The SSS family is within the APC Superfamily. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system. Members of the SSS family have been identified in bacteria, archaea and eukaryotes. Almost all functionally well-characterized members normally catalyze solute uptake via Na+ symport.

The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily. FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea, yeast, plants and lower eukaryotes. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.

<span class="mw-page-title-main">Aquaporin-6</span> Protein-coding gene in the species Homo sapiens

Aquaporin-6, (AQP-6) also known as kidney-specific aquaporin is a protein in humans that is encoded by the AQP6 gene.

<span class="mw-page-title-main">Glymphatic system</span> System for waste clearance in the central nervous system of vertebrates

The glymphatic system is a system for waste clearance in the central nervous system (CNS) of vertebrates. According to this model, cerebrospinal fluid (CSF) flows into the paravascular space around cerebral arteries, combining with interstitial fluid (ISF) and parenchymal solutes, and exiting down venous paravascular spaces. The pathway consists of a para-arterial influx route for CSF to enter the brain parenchyma, coupled to a clearance mechanism for the removal of interstitial fluid (ISF) and extracellular solutes from the interstitial compartments of the brain and spinal cord. Exchange of solutes between CSF and ISF is driven primarily by arterial pulsation and regulated during sleep by the expansion and contraction of brain extracellular space. Clearance of soluble proteins, waste products, and excess extracellular fluid is accomplished through convective bulk flow of ISF, facilitated by astrocytic aquaporin 4 (AQP4) water channels.

Ralf Kaldenhoff (* 2 October 1958) is a German botanist and professor for applied plant sciences at the Technische Universität Darmstadt. He is known for his work on the aquaporin protein class, where he detected facilitated diffusion of CO2 in plant tissue and cells and in chloroplasts respectively.

Members of the Non-Selective Cation Channel-2 (NSCC2) Family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretory systems of yeast microsomes. They are also the non-selective (NS) cation channels of the mammalian cytoplasmic membrane.

References

  1. ↑ Fu D, Libson A, Miercke LJ, et al. (October 2000). "Structure of a glycerol-conducting channel and the basis for its selectivity". Science. 290 (5491): 481–6. Bibcode:2000Sci...290..481F. doi:10.1126/science.290.5491.481. PMID   11039922.
  2. 1 2 Benga, Gheorghe (2012-12-01). "On the definition, nomenclature and classification of water channel proteins (aquaporins and relatives)". Molecular Aspects of Medicine. 33 (5–6): 514–517. doi:10.1016/j.mam.2012.04.003. ISSN   1872-9452. PMID   22542572.
  3. ↑ Reizer J, Reizer A, Saier Jr MH (1993). "The MIP family of integral membrane channel proteins: sequence comparisons, evolutionary relationships, reconstructed pathway of evolution, and proposed functional differentiation of the two repeated halves of the proteins". Crit. Rev. Biochem. Mol. Biol. 28 (3): 235–257. doi:10.3109/10409239309086796. PMID   8325040.
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  5. ↑ Finn, Roderick Nigel; Chauvigné, François; Stavang, Jon Anders; Belles, Xavier; Cerdà, Joan (2015-01-01). "Insect glycerol transporters evolved by functional co-option and gene replacement". Nature Communications. 6: 7814. Bibcode:2015NatCo...6.7814F. doi:10.1038/ncomms8814. ISSN   2041-1723. PMC   4518291 . PMID   26183829.
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  14. ↑ Rao, Y.; Bodmer, R.; Jan, L. Y.; Jan, Y. N. (1992-09-01). "The big brain gene of Drosophila functions to control the number of neuronal precursors in the peripheral nervous system". Development. 116 (1): 31–40. doi:10.1242/dev.116.1.31. ISSN   0950-1991. PMID   1483394.
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  16. ↑ Pareek, Gautam; Krishnamoorthy, Vivekanandhan; D'Silva, Patrick (2013-12-01). "Molecular insights revealing interaction of Tim23 and channel subunits of presequence translocase". Molecular and Cellular Biology. 33 (23): 4641–4659. doi:10.1128/MCB.00876-13. ISSN   1098-5549. PMC   3838011 . PMID   24061477.
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  19. ↑ Verma, Ravi Kumar; Gupta, Anjali Bansal; Sankararamakrishnan, Ramasubbu (2015-01-01). Major intrinsic protein superfamily: channels with unique structural features and diverse selectivity filters. Methods in Enzymology. Vol. 557. pp. 485–520. doi:10.1016/bs.mie.2014.12.006. ISBN   9780128021835. ISSN   1557-7988. PMID   25950979.
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  21. ↑ Heller, K. B.; Lin, E. C.; Wilson, T. H. (1980-10-01). "Substrate specificity and transport properties of the glycerol facilitator of Escherichia coli". Journal of Bacteriology. 144 (1): 274–278. doi:10.1128/JB.144.1.274-278.1980. ISSN   0021-9193. PMC   294637 . PMID   6998951.
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  23. ↑ Beese-Sims, Sara E.; Lee, Jongmin; Levin, David E. (2011-12-01). "Yeast Fps1 glycerol facilitator functions as a homotetramer". Yeast. 28 (12): 815–819. doi:10.1002/yea.1908. ISSN   1097-0061. PMC   3230664 . PMID   22030956.
  24. ↑ Fu, D.; Libson, A.; Miercke, L. J.; Weitzman, C.; Nollert, P.; Krucinski, J.; Stroud, R. M. (2000-10-20). "Structure of a glycerol-conducting channel and the basis for its selectivity". Science. 290 (5491): 481–486. Bibcode:2000Sci...290..481F. doi:10.1126/science.290.5491.481. ISSN   0036-8075. PMID   11039922.
  25. ↑ Hub, Jochen S.; de Groot, Bert L. (2008-01-29). "Mechanism of selectivity in aquaporins and aquaglyceroporins". Proceedings of the National Academy of Sciences of the United States of America. 105 (4): 1198–1203. Bibcode:2008PNAS..105.1198H. doi: 10.1073/pnas.0707662104 . ISSN   1091-6490. PMC   2234115 . PMID   18202181.
  26. ↑ Murata, K.; Mitsuoka, K.; Hirai, T.; Walz, T.; Agre, P.; Heymann, J. B.; Engel, A.; Fujiyoshi, Y. (2000-10-05). "Structural determinants of water permeation through aquaporin-1". Nature. 407 (6804): 599–605. Bibcode:2000Natur.407..599M. doi:10.1038/35036519. ISSN   0028-0836. PMID   11034202. S2CID   4402613.
  27. ↑ Jiang, Jiansheng; Daniels, Brenda V.; Fu, Dax (2006-01-06). "Crystal structure of AqpZ tetramer reveals two distinct Arg-189 conformations associated with water permeation through the narrowest constriction of the water-conducting channel". The Journal of Biological Chemistry. 281 (1): 454–460. doi: 10.1074/jbc.M508926200 . ISSN   0021-9258. PMID   16239219.
  28. ↑ Törnroth-Horsefield, Susanna; Wang, Yi; Hedfalk, Kristina; Johanson, Urban; Karlsson, Maria; Tajkhorshid, Emad; Neutze, Richard; Kjellbom, Per (2006-02-09). "Structural mechanism of plant aquaporin gating". Nature. 439 (7077): 688–694. Bibcode:2006Natur.439..688T. doi:10.1038/nature04316. ISSN   1476-4687. PMID   16340961. S2CID   4365486.
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