VariO protein structure annotation examples

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Examples of annotation of protein structure variation using the Variation Ontology VariO.


All these examples are discussed in Vihinen, M., in press. Types and effects of protein variations

The root terms for these examples are (hovering over the terms will show you the definition of the term):

VariO:0002 variation affecting protein

VariO:0060 variation affecting protein structure

VariO:0064 effect on protein 3D structure

VariO:0065 effect on protein dynamics

ECO:0000122 protein localization evidence
Experimental method used: site-directed fluorescence labeling (SDFL) spectroscopy

Proteins are dynamic molecules and in constant motion but the basic scaffolding usually remains the same during the fluctuations. Variations can affect normal dynamics in several ways. The M257Y substitution is a constitutively active variant of the G-protein coupled receptor (GPCR) that affects the dynamics of the structural alteration between the active and inactive conformation. The transition is essential for the protein function. The protein with the gain of function variant is in the active conformation even in the absence of the activating external signal.
PUBMED

VariO:0069 effect on allosteric site

ECO:0000122 protein localization evidence

A P275L substitution in phenylalanine hydroxylase (PAH) has an “effect on the allosteric site” regulation by cofactor causing phenolketonuria (PKU), a metabolic disorder, which, if untreated, leads to intellectual disability, seizures and other problems. PAH is needed to degrade phenylalanine to tyrosine. The variant has a decreased affinity for the cofactor tetrahydrobiopterin, thereby disturbing allostery. The substrate affinity, however, is even increased. PKU is the most common inborn error in amino acid metabolism in European descent populations.
PUBMED

VariO:0067 effect on induced fit

ECO:0000184 enzyme inhibition evidence

Apurinic/apyrimidinic endonuclease 1 (APE1) is required for DNA damage correction by base excision and nucleotide incision repair mechanisms. The enzyme-substrate complex undergoes induced fit upon binding to lesion. Substitution K98A in APE1 has an “effect on induced fit” preventing it and decreasing the stability of enzyme-substrate complex.
PUBMED

VariO:0068 effect on structural disorder

Experimental method used: modelling

Protein structures typically fold to ordered 3D structures. Exceptions are intrinsically disordered proteins and regions. Disordered regions can adopt diverse temporary conformations and have large numbers of binding partners. An example is tumor suppressor p53, which contains large disordered regions that interact with several different partners. Variations at p53 are hallmarks in numerous cancers. “Effect on structural disorder” status is related to certain diseases.
PUBMED

Misfolded proteins have four possible fates in cells. They are either degraded, refolded, they form aggregates or they are sequestered. The single amino acid replacement D54G in creatine kinase leads to muscle creatine kinase deficiency. The variant has a partially misfolded structure, and although the protein is produced, the activity is impaired. Creatine kinase catalyzes the production of ATP by transferring phosphate group from phosphoserine. Muscles, especially heart, consume lots of high energy ATP molecules.
PUBMED

VariO:0066 effect on structural flexibility

Laforin regulates cellular autophagy. Harmful variations are responsible for the progressive form of myoclonus epilepsy called Lafora disease. The K87A substitution in laforin has reduced stability due to “effect on structural flexibility”. Laforin has two activities, protein dual specificity phosphatase and glycogen binding. K87A eliminates the glycogen binding activity without an effect on phosphatase activity. This is because the activities are in different domains.
PUBMED

VariO:0070 effect on protein tertiary structure

VariO:0114 effect on amino acid size

VariO:0115 effect on protein packing

VariO:0116 protein cavity formation

ECO:0000039 protein assay evidence

An I2A substitution of the invariant residue in chain A of insulin generates a cavity into the hydrophobic protein core and leads to reduced thermal stability.
PUBMED

VariO:0117 protein overpacking

Overpacking appears when the variant is larger than the original residue which leads to sterical clashes and at least local structural change. The larger side chain of the G584W substitution does not fit into the core of the BTK kinase domain structure without structural alterations due to clashes with a large number of amino acids.
PUBMED

VariO:0071 effect on protein folding rate

Protein folding is a complex process, the rate of which can be altered by variations. Even minor amino acid substitutions including Y25F and V68A have major effects to the folding rate of muscle acylphosphatase (AcP). AcP is a widely studied model because it folds slowly and is thus easy to investigate.
PUBMED

VariO:0118 effect on protein interaction site

VariO:0119 effect on protein binding site

Type I interferons (IFNs) are cytokines having immunomodulatory, antiviral and antiproliferative activities. Substitution R120A and variations at surrounding amino acids in the α-helix D in human IFNα2 have “effect on protein binding site” by decreasing interaction with receptor subdomain IFNAR-1 while the affinity for IFNAR-2 subunit remains unchanged
PUBMED

VariO:0120 effect on protein catalytic site

An example of variation having an “effect on protein catalytic site” is BTK in which variants R525Q and D430E at catalytic amino acids cause XLA.
PUBMED

VariO:0107 effect on protein post translational modification

VariO:0108 deletion of a post translational modification site

ECO:0000046 protein expression level evidence

Numerous proteins are post-translationally modified after synthesis. These modifications often have important regulatory functions. “Deletion of post translational modification site” can occur due to a variation. The BTK kinase domain is activated by Y551 phosphorylation at the activation loop. Variation Y551H inactivates the protein by preventing activation although the protein is expressed.
PUBMED

VariO:0113 generation of a novel post translational modification site

ECO:0000112 Western blot evidence

A T168N substitution leads to “generation of a novel post translational modification site”, a new N-glycosylation site, to interferon receptor IFNγR2 causing severe mycobacterial disease. Because the variant protein contains an extra carbohydrate moiety it has an increased molecular weight.
PUBMED

VariO:0109 effect on protein processing

VariO:0111 variation generating a novel protein processing site

ECO:0000112 Western blot evidence

Proteolytic processing is a common mechanism in protein activation and thus variations can have an “effect on protein processing”. “Effect on protein splicing” does not occur in human, but in some other organisms. Indel I143NT in the Ca2+-binding loop of guanylate cyclase-activating protein 1 (GCAP1) confers the protein susceptible for proteolysis and is thus annotated as “variation generating a novel protein processing site”. The variant leads to autosomal dominant cone degenerate in retinal diseases.
PUBMED

VariO:0112 variation preventing polypeptide processing

ECO:0000007 immunofluorescence evidence

Variation R628P in integrin α3β1, which acts as receptor for laminins, is a “variation preventing polypeptide processing” of seven-bladed β-propeller structure of the protein. Upon maturation, the propeller structure is cleaved to produce heavy and light chains, which remain connected by a disulfide bond. The protein transport to the cell surface is deficit from endoplasmic reticulum (ER) to Golgi apparatus. The variant is associated with disorders in the lung, kidney, and skin due to its wide expression during development in epithelic organs.
PUBMED

VariO:0121 effect on protein quaternary structure

VariO:0122 effect on protein quaternary structure forming interaction

ECO:0000082 polymerase chain reaction evidence

ECO:0000046 protein expression level evidence

ECO:0000039 protein assay evidence

Protein quaternary structures are formed of interacting subunits. Variations with an “effect on quaternary structure forming interaction” can be harmful by preventing or weakening complex formation. A congenital cataract-causing A2V substitution in the eye lens βB2-crystallin folds normally and forms a βB2/βA3-crystallin dimer, however it prevents tetramer formation, the protein complex in eyes.
PUBMED