Porins are
beta barrel
In protein structures, a beta barrel is a beta sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are ...
proteins that cross a
cellular membrane
The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment (th ...
and act as a pore, through which
molecules can
diffuse
Diffusion is the net movement of anything (for example, atoms, ions, molecules, energy) generally from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in Gibbs free energy or chemical p ...
. Unlike other
membrane transport protein
A membrane transport protein (or simply transporter) 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 transmembra ...
s, porins are large enough to allow passive diffusion, i.e., they act as
channels
Channel, channels, channeling, etc., may refer to:
Geography
* Channel (geography), in physical geography, a landform consisting of the outline (banks) of the path of a narrow body of water.
Australia
* Channel Country, region of outback Austral ...
that are specific to different types of molecules. They are present in the
outer membrane of
gram-negative bacteria
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
and some
gram-positive
In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
Gram-positive bact ...
mycobacteria (mycolic acid-containing
actinomycetes
The Actinomycetales is an order of Actinomycetota. A member of the order is often called an actinomycete. Actinomycetales are generally gram-positive and anaerobic and have mycelia in a filamentous and branching growth pattern. Some actinomycete ...
), the outer membrane of
mitochondria, and the
outer chloroplast membrane (outer plastid membrane).
Structure
Porins are composed of
beta sheets (β sheets) made up of
beta strand
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
s (β strands) which are linked together by beta turns on the
cytoplasm
In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. ...
ic side and long loops of
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...
s on the other. The β strands lie in an
antiparallel fashion and form a cylindrical tube, called a
beta barrel
In protein structures, a beta barrel is a beta sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are ...
(β barrel).
The amino acid composition of the porin β strands are unique in that polar and nonpolar residues alternate along them. This means that the nonpolar residues face outward so as to interact with the
nonpolar
In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end.
Polar molecules must contain one or more polar ...
lipid
Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids includ ...
s of
outer membrane, whereas the polar residues face inwards into the center of the beta barrel to create the
aqueous
An aqueous solution is a solution in which the solvent is water. It is mostly shown in chemical equations by appending (aq) to the relevant chemical formula. For example, a solution of table salt, or sodium chloride (NaCl), in water would be re ...
channel. The specific amino acids in the channel determine the specificity of the porin to different molecules.
The β barrels that make up a porin are composed of as few as eight β strands to as many as twenty-two β strands. The individual strands are joined together by loops and turns. The majority of porins are
monomer
In chemistry, a monomer ( ; '' mono-'', "one" + ''-mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or three-dimensional network in a process called polymerization.
Classification
...
s; however, some
dimeric porins have been discovered, as well as an
octameric porin. Depending on the size of the porin, the interior of the protein may either be filled with water, have up to two β strands folded back into the interior, or contain a "stopper" segment composed of β strands.
All porins form homotrimers in the outer membrane, meaning that three identical porin subunits associate together to form a porin super-structure with three channels.
Hydrogen bonding and
dipole-dipole interactions between each monomer in the homotrimer ensure that they do not dissociate, and remain together in the outer membrane.
Several parameters have been used to describe the structure of a porin protein. They include the tilting angle (α), shear number (S), strand number (n), and barrel radius (R).
The tilting angle refers to the angle relative to the membrane. The shear number (S) is the number of amino acid residues found in each β strands. Strand number (n) is the amount of β strands in the porin, and barrel radius (R) refers to the radius of the opening of the porin. These parameters are related via the following formulas:
:
and,
:
Using these formulas, the structure of a porin can be determined by knowing only a few of the available parameters. While the structure of many porins have been determined using
X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
, the alternative method of sequencing
protein primary structure may also be used instead.
Cellular roles
Porins are water-filled pores and channels found in the membranes of bacteria and eukaryotes. Porin-like channels have also been discovered in archaea.
Note that the term "
nucleoporin
Nucleoporins are a family of proteins which are the constituent building blocks of the nuclear pore complex (NPC). The nuclear pore complex is a massive structure embedded in the nuclear envelope at sites where the inner and outer nuclear membra ...
" refers to unrelated proteins that facilitate transport through nuclear pores in the
nuclear envelope.
Porins are primarily involved in passively transporting
hydrophilic
A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press.
In contrast, hydrophobes are ...
molecules of various sizes and charges across the membrane.
For survival, certain required nutrients and substrates must be transported into the cells. Likewise, toxins and wastes must be transported out to avoid toxic accumulation.
Additionally, porins can regulate permeability and prevent lysis by limiting the entry of detergents into the cell.
Two types of porins exist to transport different materials– general and selective. General porins have no substrate specificities, though some exhibit slight preferences for anions or cations.
Selective porins are smaller than general porins, and have specificities for chemical species. These specificities are determined by the threshold sizes of the porins, and the amino acid residues lining them.
In
gram-negative bacteria
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
, the inner membrane is the major permeability barrier.
The outer membrane is more permeable to hydrophilic substances, due to the presence of porins.
Porins have threshold sizes of transportable molecules that depend on the type of bacteria and porin. Generally, only substances less than 600
Daltons in size can diffuse through.
Diversity
Porins were first discovered in gram-negative bacteria, but
gram-positive bacteria with both types of porins have been found.
They exhibit similar transport functions but have a more limited variety of porins, compared to the distribution found in gram-negative bacteria.
Gram-positive bacteria lack outer membranes, so these porin channels are instead bound to specific lipids within the cell walls.
Porins are also found in eukaryotes, specifically in the outer membranes of
mitochondria and
chloroplasts
A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
.
The organelles contain general porins that are structurally and functionally similar to bacterial ones. These similarities have supported the
Endosymbiotic theory, through which eukaryotic organelles arose from gram-negative bacteria.
However, eukaryotic porins exhibit the same limited diversity as gram-positive porins, and also display a greater voltage-dependent role during metabolism.
Archaea also contain ion channels that have originated from general porins.
The channels are found in the cell envelope and help facilitate solute transfer. They have similar characteristics as bacterial and mitochondrial porins, indicating physiological overlaps over all three domains of life.
Antibiotic resistance
Many porins are targets for host immune cells, resulting in
signaling pathways
Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellula ...
that lead to bacterial degradation. Therapeutic treatments, like vaccinations and antibiotics, are used to supplement this immune response.
Specific antibiotics have been designed to travel through porins in order to inhibit cellular processes.
However, due to selective pressure, bacteria can develop resistance through mutations in the porin gene.
The mutations may lead to a loss of porins, resulting in the antibiotics having a lower permeability or being completely excluded from transport. These changes have contributed to the global emergence of
antibiotic resistance, and an increase in mortality rates from infections.
Discovery
The discovery of porins has been attributed to Hiroshi Nikaido, nicknamed "the porinologist."
Classification
According to
TCDB, there are five evolutionarily independent
superfamilies of porins. Porin superfamily I includes 47 families of porins with a range of numbers of
trans-membrane β-strands (β-TMS). These include the GBP, SP and RPP porin families. While PSF I includes 47 families, PSF II-V each contain only 2 families. While PSF I derives members from
gram-negative bacteria
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
primarily one family of eukaryotic mitochondrial porins, PSF II and V porins are derived from
Actinomycetota
The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to s ...
. PSF III and V are derived from eukaryotic organelle.
Porin Superfamily I
1.B.1 - The
General bacterial porin family
1.B.2 - The Chlamydial Porin (CP) Family
1.B.3 - The
Sugar porin (SP) Family
1.B.4 - The ''
Brucella-Rhizobium porin'' (BRP) Family
1.B.5 - The ''Pseudomonas'' OprP Porin (POP) Family
1.B.6 -
OmpA-OmpF porin (OOP) family
1.B.7 ''Rhodobacter'' PorCa porin (RPP) family
1.B.8
Mitochondrial and plastid porin (MPP) family
1.B.9
FadL outer membrane protein (FadL) family
1.B.10
Nucleoside-specific channel-forming outer membrane porin (Tsx) family
1.B.11 Outer membrane fimbrial usher porin (FUP) family
1.B.12
Autotransporter-1 (AT-1) family
1.B.13
Alginate export porin (AEP) family
1.B.14
Outer membrane receptor (OMR) family
1.B.15 Raffinose porin (RafY) family
1.B.16 Short chain amide and urea porin (SAP) family
1.B.17
Outer membrane factor (OMF) family
1.B.18
Outer membrane auxiliary (OMA) protein family
1.B.19 Glucose-selective OprB porin (OprB) family
1.B.20 Two-partner secretion (TPS) family
1.B.21
OmpG porin (OmpG) family
1.B.22 Outer bacterial membrane secretin (secretin) family
1.B.23 Cyanobacterial porin (CBP) family
1.B.24
Mycobacterial porin
1.B.25
Outer membrane porin (Opr) family
1.B.26 Cyclodextrin porin (CDP) family
1.B.31 ''
Campylobacter jejuni
''Campylobacter jejuni'' () is a species of pathogenic bacteria, one of the most common causes of food poisoning in Europe and in the US. The vast majority of cases occur as isolated events, not as part of recognized outbreaks. Active surveillan ...
'' major outer membrane porin (MomP) family
1.B.32 Fusobacterial outer membrane porin (FomP) family
1.B.33 Outer membrane protein insertion porin (Bam complex) (OmpIP) family
1.B.34
Corynebacterial porins
1.B.35
Oligogalacturonate-specific porin (KdgM) family
1.B.39
Bacterial porin, OmpW (OmpW) family
1.B.42 - The Outer Membrane Lipopolysaccharide Export Porin (LPS-EP) Family
1.B.43 - The ''Coxiella'' Porin P1 (CPP1) Family
1.B.44 - The Probable Protein Translocating ''Porphyromonas gingivalis'' Porin (PorT) Family
1.B.49 - The ''Anaplasma'' P44 (A-P44) Porin Family
1.B.54 -
Intimin
Intimin is a virulence factor ( adhesin) of EPEC (''e.g.'' ''E. coli'' O127:H6) and EHEC (''e.g. E. coli'' O157:H7) '' E. coli'' strains. It is an attaching and effacing (A/E) protein, which with other virulence factors is necessary and respons ...
/Invasin (Int/Inv) or
Autotransporter-3 family
1.B.55 - The Poly Acetyl Glucosamine Porin (PgaA) Family
1.B.57 - The Legionella Major-Outer Membrane Protein (LM-OMP) Family
1.B.60 - The Omp50 Porin (Omp50 Porin) Family
1.B.61 - The Delta-Proteobacterial Porin (Delta-Porin) Family
1.B.62 - The Putative Bacterial Porin (PBP) Family
1.B.66 - The Putative Beta-Barrel Porin-2 (BBP2) Family
1.B.67 - The Putative Beta Barrel Porin-4 (BBP4) Family
1.B.68 - The Putative Beta Barrel Porin-5 (BBP5) Superfamily
1.B.70 - The Outer Membrane Channel (OMC) Family
1.B.71 - The Proteobacterial/Verrucomicrobial Porin (PVP) Family
1.B.72 - The Protochlamydial Outer Membrane Porin (PomS/T) Family
1.B.73 - The Capsule Biogenesis/Assembly (CBA) Family
1.B.78 - The DUF3374 Electron Transport-associated Porin (ETPorin) Family
Porin Superfamily II (MspA Superfamily)
1.B.24 -
Mycobacterial porin
1.B.58 - Nocardial Hetero-oligomeric Cell Wall Channel (NfpA/B) Family
Porin Superfamily III
1.B.28 - The Plastid Outer Envelope Porin of 24 kDa (OEP24) Family
1.B.47 - The Plastid Outer Envelope Porin of 37 kDa (OEP37) Family
Porin Superfamily IV (Tim17/OEP16/PxMPL (TOP) Superfamily)
This superfamily includes protein that comprise pores in multicomponent protein translocases as follows: 3.A.8 -
im17 (P39515) Tim22 (Q12328) Tim23 (P32897) 1.B.69 -
XMP4 (Q9Y6I8) PMP24 (A2R8R0) 3.D.9 -
DH 21.3 kDa component (P25710)
1.B.30 - The Plastid Outer Envelope Porin of 16 kDa (OEP16) Family
1.B.69 - The Peroxysomal Membrane Porin 4 (PxMP4) Family
3.A.8 - The
Mitochondrial Protein Translocase (MPT) Family
Porin Superfamily V (Corynebacterial PorA/PorH Superfamily)
1.B.34 - The Corynebacterial Porin A (PorA) Family
1.B.59 - The Outer Membrane Porin, PorH (PorH) Family
See also
*
Voltage-dependent anion channel
Voltage-dependent anion channels, or mitochondrial porins, are a class of porin ion channel located on the outer mitochondrial membrane. There is debate as to whether or not this channel is expressed in the cell surface membrane.
This major pro ...
*
Aquaporin
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 ...
References
External links
Overviewat
University of Hamburg
The University of Hamburg (german: link=no, Universität Hamburg, also referred to as UHH) is a public research university in Hamburg, Germany. It was founded on 28 March 1919 by combining the previous General Lecture System ('' Allgemeines Vo ...
* - OmpG porin
* - Trimeric porins
* - Sugar porins
{{DEFAULTSORT:Porin (Protein)
Transmembrane proteins
Outer membrane proteins