SNAP47

Key takeaways

SNAP47 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect SNAP47 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of SNAP47 from memory before moving on to harder problems.

Reference excerpt

Synaptosome-associated protein, 47 kDal (SNAP47) is a human protein encoded by the SNAP47 gene. Other aliases of this gene are SVAP1, HEL170, ESFI5812, and HEL-S-290. SNAP47 is a synaptosome protein which is associated with the protein coding in multiple diseases, including non small cell lung cancer and schizophrenia. SNAP47 is a member of the SNAP protein family. SNAP proteins are t-snare proteins that are a component of SNARE complex. The SNARE complex mediates vesicle fusion by creating tight complex that brings vesicle and membrane together. This protein causes ubiquitous expression in testis, ovary, and many other tissues

Gene The gene is located at 1q42.13, meaning on chromosome 1 on the long arm of the chromosome in region 42, sub region 13. There are a total of 13 exons and 12 introns. This gene spans 52,693 base pairs. It is encoded on the plus strand. The coordinates for this gene are 227728518-227781231. The gene is flanked by ZNF678 gene and PRSS38 gene on the chromosome while the same location on the minus strand JMJD4 gene.

Protein The most common isoform of SNAP47 is 419 amino acids long. SNAP47 protein is a synaptosome associated protein. Its molecular weight has been found to be 47167 M. SNARE complex (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) includes syntaxin proteins, VAMP proteins and SNAP proteins. SNARE proteins are generally known to be related to vesicle fusion - mediating exocytosis or neurotransmitter release.

They have also been associated with BLOC-1 (biogenesis of lysosome-related organelles complex-1). Hippocampal neurons deficient in BLOC-1 suggest neurite outgrowth defects which when taken with association of SNARE leads to possible variants of genes encoding BLOC-1 - DTNBP1 - in Schizophrenia models.

Secondary structure The secondary structure of SNAP47 has some long alpha helices intermixed with beta sheet and random coils. The alpha helix are placed at about amino acid 120-150 and amino acids 350-415. SNARE proteins are believed to form compact four-helix complex with membranes. The two alpha helices found are consistent with this observation.

Tertiary structure I-TASSER assembled and then aligned possible SNAP47 tertiary sequence with 5VOX, a Yeast V-ATPase, and a Ufd2 complexed with ubiquitin-like domain Rad23. The TM scores respectively were 0.917 and 0.584.

Regulation of gene expression

Gene level regulation

Promoter SNAP47 carries 4 promoter regions that create different variants of transcription. These were identified using by Eldorado at Genomatix. Promoter B boosts transcript variant 2 - GXT_27753855.

Transcription factors Transcription Factors that have been predicted to attach to the promoter for SNAP47 are SP1, TATAB, and CARF. SP1 or Stimulating protein 1 had a matrix similarity of 1.0 and is a ubiquitous zinc finger transcription factor and is on the minus strand. TATAB is a TATA binding protein factor with a similar matrix of 0.945. CARF is a calcium response element with a matrix similarity of 0.928. SNAP25 decreases Ca2+ responsiveness in GABAargic synapses.

Expression pattern RNAseq data display SNAP47 to be highly expressed in the adrenal gland, fetal brain, adult brain and the heart. The adrenal gland, hormone producer, was transcribed at 8 reads per kilobase per million (RPKM). The lungs transcription is relatively low transcription except in a 17-week-old fetus. The transcription of the 17-week-old fetus lung is above 2 RPKM. There is low transcription rate (below 2 RPKM) found in the fetal liver, trachea, pancreas and bone marrow. In the cell, SNAP47 localizes cytoplasm, the endoplasmic reticulum (ER), and Vesicular-tubular cluster (ERGIC). The protein abundance is about average when compared to all the other proteins in humans. However, the mRNA has a higher than average abundance seen in this microarray. The mRNA is at or above the 75th percentile in the microarray for most of the tissues tested. This may suggest that there is a larger expression rate but the protein is used up quickly for its function.

Protein level regulation

Post-transnational modification SNAP47 had multiple possible post-translational modifications. High conserved phosphorylation sites were predicted at Y15, S129, S262, and S284 - none with specific kinases. Protein Kinase C plays a role in several signal transduction cascades including calcium release. They had had scores of 0.830, 0.747, and 0.812 at S82, S223, and S231 respectively. Palmitoylation sites are important in anchoring the SNARE complex to the cytosolic side of membranes. Since many SNAP proteins do not have trans-membrane domains, these are common way of attachment. The Palitic acid is covalently attaches to a cysteine residue. Two Palmitoylation sites were predicted at the beginning of SNAP47 protein at Cys6 and Cys12. Propeptide cleavage site was predicted at R417 while an acetylation was predicted on S2.

Homology and evolution

Orthologs As of June 2020, SNAP47 is conserved in 310 orthologs. C. lupus, a wolf/dog, has a 74.2% identity. M. mulatta, a monkey, was aligned with the Homo sapiens protein transcript and a 67.1% identical amino acids were found. P. Marinus, a sea lamprey, is the most distant ortholog found at a 36.1% sequence identity. It was conserved in eukaryotes but not bacteria or Archaea. A selected list of orthologs obtained are shown below.

Paralogs SNAP47 has 3 known paralogs - SNAP23, SNAP25, SNAP 29. The sequence similarity and identity is lower than 30% for all three. This suggest low relationship between different SNAP proteins. SNAP23 and SNAP25 were 55% identical suggesting the relationship between those two paralogs are higher. There is some evidence that if SNAP29 was incapacitated, SNAP47 would be able to take over function of vesicle fusion however, it would not be efficient or successful.

Function/biochemistry

The paralogs, SNAP23 and SNAP25 are t-SNARE proteins, meaning it is present on the presynaptic plasma membrane that is being fused to (the target). These proteins bind to syntaxin protein that attaches to the membrane. SNAP29, however, is binds to syntaxin on vesicles membranes rather than to plasma membranes. SNAP29 has also been found to be membrane bound with a large amount sticking into the cytoplasm.

… excerpt ends here. Continue reading the full article.

Illustrations

Worked examples

Example 1 — a first encounter with SNAP47

Start with the simplest possible case. Write down what SNAP47 claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to SNAP47 before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about SNAP47 ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of SNAP47

In research: SNAP47 appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses SNAP47 in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: SNAP47 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genes on human chromosome 1, Proteins, so understanding it makes those chapters shorter.
In everyday life: Look for SNAP47 outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study SNAP47 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SNAP47 means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain SNAP47 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SNAP47 in simple terms?

Synaptosome-associated protein, 47 kDal (SNAP47) is a human protein encoded by the SNAP47 gene. Other aliases of this gene are SVAP1, HEL170, ESFI5812, and HEL-S-290.

Why does SNAP47 matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study SNAP47?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on SNAP47.