molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...

, alanine scanning is a

site-directed mutagenesis Site-directed mutagenesis is a molecular biology method that is used to make specific and intentional mutating changes to the DNA sequence of a gene and any gene products. Also called site-specific mutagenesis or oligonucleotide-directed mutagenesi ...

technique used to determine the contribution of a specific residue to the stability or function of a given protein.

Alanine Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side c ...

is used because of its non-bulky, chemically inert, methyl functional group that nevertheless mimics the

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

preferences that many of the other amino acids possess. Sometimes bulky amino acids such as

valine Valine (symbol Val or V) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH3+ form under biological conditions), an α- carboxylic acid group (which is in the deprotonat ...

leucine Leucine (symbol Leu or L) is an essential amino acid that is used in the biosynthesis of proteins. Leucine is an α-amino acid, meaning it contains an α-amino group (which is in the protonated −NH3+ form under biological conditions), an α- ca ...

are used in cases where conservation of the size of mutated residues is needed. This technique can also be used to determine whether the

side chain In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called the "main chain" or backbone. The side chain is a hydrocarbon branching element of a molecule that is attached to a l ...

of a specific

residue Residue may refer to: Chemistry and biology * An amino acid, within a peptide chain * Crop residue, materials left after agricultural processes * Pesticide residue, refers to the pesticides that may remain on or in food after they are applied ...

plays a significant role in

bioactivity In pharmacology, biological activity or pharmacological activity describes the beneficial or adverse effects of a drug on living matter. When a drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or ph ...

. This is usually accomplished by

or randomly by creating a PCR

library A library is a collection of materials, books or media that are accessible for use and not just for display purposes. A library provides physical (hard copies) or digital access (soft copies) materials, and may be a physical location or a vir ...

. Furthermore, computational methods to estimate thermodynamic parameters based on theoretical alanine substitutions have been developed. This technique is rapid, because many side chains are analyzed simultaneously and the need for protein purification and biophysical analysis is circumvented. The technology is very mature at this point and is widely used in biochemical fields. The data can be tested by IR,

NMR Spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fiel ...

, mathematical methods, bioassays, etc. One good example of alanine scanning is the examination of the role of charged residues on the surface of proteins. In a systematic study on the roles of conserved charged residues on the surface of epithelial sodium channel (

ENaC The epithelial sodium channel (ENaC), (also known as amiloride-sensitive sodium channel) is a membrane-bound ion channel that is selectively permeable to sodium ions (). It is assembled as a heterotrimer composed of three homologous subunits α ...

), alanine scanning was used to reveal the importance of charged residues for the process of transport of the proteins to the cell surface.

Applications

Alanine Scanning was used to determine simultaneously the functional contributions of 19 side chains buried at the interface between human growth hormone and the extracellular domain of its receptor. Each amino acid in the side chains was substituted by alanine. Then shotgun scanning method which combines the concepts of alanine scanning

mutagenesis Mutagenesis () is a process by which the genetic information of an organism is changed by the production of a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using la ...

and binomial mutagenesis with phage display technology was used. Another critical application of alanine scanning is to determine the influence of individual residues on structure and activity in the prototypic

cyclotide In biochemistry, cyclotides are small, disulfide-rich peptides isolated from plants. Typically containing 28-37 amino acids, they are characterized by their head-to-tail cyclised peptide backbone and the interlocking arrangement of their three ...

kalata B1. Cyclotides display a wide range of pharmaceutically important bioactivities, but their natural function is in plant defense as insecticidal agents. On the structure of cyclotides kalata B1, all 23 non-cysteine residues were successively substituted with alanine. The data were tested by

. In addition, alanine scanning is also used to determine which functional motif of Cry4Aa has the mosquitocidal activity. Cry4Aa was produced by ''

Bacillus thuringiensis ''Bacillus thuringiensis'' (or Bt) is a gram-positive, soil-dwelling bacterium, the most commonly used biological pesticide worldwide. ''B. thuringiensis'' also occurs naturally in the gut of caterpillars of various types of moths and butterflie ...

''. It is a dipteran-specific toxin and it plays an important role in how to produce a bioinsecticide to control mosquitoes. So, it is very essential to determine which functional motif of Cry4Aa contributes to this activity. In this study, several Cry4Aa mutants were made by replacing the residues of potential receptor binding site, loops 1, 2, and 3 in domain II with alanine. A bioassay ''

Culex pipiens ''Culex pipiens'', commonly referred to as the common house mosquito, is a species of mosquito. House mosquitoes are some of the most common mosquitoes in the United States. More specifically, ''Culex pipiens'' is considered as the northern hous ...

'' was followed to test the activities.

Alanine-World model

The alanine scanning method takes advantage of the fact that most canonical amino acids can be exchanged with Ala by point mutations, while the

of mutated protein remains intact, as Ala mimics the secondary structure preferences of the majority of the encoded or canonical amino acids. This is predicted by the Alanine-World model.

Applications

Alanine-World model

References

Further reading