How is membrane protein topology determined?
In determining membrane protein topology using epitope tagging (see Support Protocol), a foreign epitope is placed within the sequence of a membrane protein. The topology of the domain containing the inserted epitope can then be determined using protease digestion or immunofluorescence staining.
What is membrane protein topology?
Membrane topology refers to the two-dimensional structural information of a membrane protein that indicates the number of transmembrane (TM) segments and the orientation of soluble domains relative to the plane of the membrane.
What is topology in protein structure?
The topology of a protein structure is a highly simplified description of its fold including only the sequence of secondary structure elements, and their relative spatial positions and approximate orientations. This information can be embodied in a two-dimensional diagram of protein topology, called a TOPS cartoon.
How do you identify membrane proteins?
Tandem mass spectrometry analysis equipped with a MALDI or ESI ion source is often used for membrane protein identification. Peptides were analyzed by mass spectrometry and obtain mass spectra. Subsequently, the bioinformatics tools and software (such as Mascot) are used for membrane protein identification.
What are membrane spanning proteins?
Membrane-spanning protein channels and pores play critical roles in cellular functions, transporting ions and small molecules across biological membranes [1–3]. Many of these form bundled and barrel-like structures, which are generally based on either α-helical or β-hairpin units, respectively [4].
What are membrane-spanning proteins?
How do you study membrane proteins?
Extracting, purifying, homogenizing or removing them from the membrane could mean serious loss of information and protein unwinding and unfolding. The best way to study protein membranes is to mimic their native environment in the cell, embedded or attached to the cell membrane.
How many membrane proteins are in PDB?
OPM contains 6044 unique PDB entries, many of which are monotopic or peripheral membrane proteins, as described later. In contrast, PDBTM contains only 30 unique PDB entries.
What are hydropathy plots in bioinformatics?
A hydrophilicity plot is a quantitative analysis of the degree of hydrophobicity or hydrophilicity of amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein.
What do Ramachandran plots show?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
What does spanning the membrane mean?
fully spanning plasma membrane | transmembrane. Definition: The component of the plasma membrane consisting of gene products and protein complexes that have some part that spans both leaflets of the membrane.
What is protein folding in bioinformatics?
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a “folded” conformation by which the protein becomes biologically functional.
Why is studying membrane proteins hard?
Membrane proteins have proven to be difficult to study owing to their partially hydrophobic surfaces, flexibility and lack of stability.
What is the topology of a membrane protein?
The topology of a membrane protein was just a description, listing the segments of the polypeptide chain that form the transmembrane helices and their orientation relative to the membrane. But now, 6 years on and 60 high-resolution membrane-protein structures later, the picture is not so simple.
How is topology of transmembrane helices determined?
Topology is controlled primarily by the hydrophobicity and length of transmembrane helices as well as the distribution of positively charged residues in the loops that connect the helices. In most cases, topology is determined co-translationally during the translocon-mediated insertion of a polypeptide into a membrane.
What is the best book on transmembrane protein topology?
Nature Rev. Mol. Cell. Biol. 5, 519–530 (2004). Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes. J. Mol. Biol. 305, 567–580 (2001). Daley, D. O. et al. Global topology analysis of the Escherichia coli inner membrane proteome.
How are membrane-spanning sequences identified in polytopic membrane proteins?
Sequences throughout the amino acid sequence of a polytopic membrane protein are identified that are able to insert independently of each other into the ER membrane, with a preferred orientation. Different algorithms (56, 99) that predict putative membrane-spanning sequences are used to guide the initial selection of potential candidates.