SNED1

Key takeaways

SNED1 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect SNED1 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of SNED1 from memory before moving on to harder problems.

Reference excerpt

SNED1 (Sushi, Nidogen, and EGF-like Domains) is an extracellular matrix (ECM) protein expressed at low levels in a wide range of tissues. The gene encoding SNED1 is located in the human chromosome 2 at locus q37.3. The corresponding mRNA isolated from the spleen and is 6834bp in length, and the corresponding protein is 1413 amino-acid long. The mouse ortholog of SNED1 was cloned in 2004 from the embryonic kidney by Leimester et al. SNED1 present domains characteristic of ECM proteins, including an amino-terminal NIDO domain, several calcium binding EGF-like domains (EGF_CA), a Sushi domain also known as complement control protein (CCP) domain, and three type III fibronectin (FN3) domains in the carboxy-terminal region.

Gene

Locus SNED1 is located on the plus strand of chromosome 2 at locus 2q37.3. The Refseq identification number is NM_001080437.3 The genomic DNA sequence of SNED1 contains 98,159bp and the longest spliced mRNA as predicted by AceView is 7048bp and contains 31 exons. There are 9 predicted splice variants of SNED1 that exhibited protein structure matches using the Phyre 2 database which is discussed under "Tertiary and Quaternary Structure".

Common aliases SNED1 is an acronym for Sushi, Nidogen, and EGF-like Domains 1. Obsolete aliases for SNED1 include Snep, SST3, and IRE-BP1.

Homology/evolution

Homologs and phylogeny SNED1 is highly conserved throughout evolutionary history and is shown to exhibit this conservation across vertebrates including fish, reptiles, amphibians, birds, and mammals. It is unclear that SNED1 is conserved in invertebrates, but protein domains found in SNED1 are also found in invertebrates. It may be worth noting that the abundance of cysteine residues, mostly located within EGF-like domains where they form disulfide bonds, appears to be very highly conserved, suggesting that the cysteine richness is a very important feature of this protein.

Paralogs SNED1 has several paralogs within the human genome, which cover small portions of the entire peptide sequence. Genes encoding proteins sharing domains (EGF-like, Sushi) with SNED 1 include the neurogenic locus notch homolog (NOTCH) proteins, the jagged proteins, eyes shut homolog proteins, the crumbs homolog proteins, delta and notch-like epidermal growth factor receptors, the sushi von Wilebrand factor A protein (SVEP1), and slit homolog three protein.

Protein

Primary sequence The Protein Knowledge Database, UniProt, reports that the full length SNED1 protein is 1413 amino-acid long (UniProt Q8TER0). The full sequence obtained by an NCBI BLAST search can be accessed with the reference ID NP_001073906.1. One presumably important feature of this protein that is worth noting is that it is extraordinarily cysteine rich, with 107 cysteines total, giving an overall cysteine composition of 13.2%.

Domains and motifs SNED1 is a secreted protein of the extracellular matrix. It contains a signal peptide (amino acid 1-24) directing the protein to the secretory pathway. Precise prediction of domain boundaries can be obtained using the InterPro domain database or SMART. There are various interesting domains in this protein. The first in the annotated sequence above shown in pink, is the NIDO domain, also found in the Nidogen-1 protein, also known as Entactin. Other than SNED1, this domain is shared with only four human proteins: the basement membrane proteins nidogen-1, nidogen-2, and alpha-tectorin; and mucin-4, which has been demonstrated to play a role in promoting pancreatic cancer metastasis. The second regions of interest shown by an underline are calcium-binding EGF domain (EGF-CA). There are many of these domains in the sequence and they are often present in a large number of membrane bound and extracellular proteins. These EGF-CA domains may suggest a "sticky" nature to this protein as oftentimes extracellular matrix (ECM) proteins require calcium cations to form homo- and hetero-dimeric complexes between other ECM proteins. The Sushi domain or complement control protein (CCP) motif is annotated in green in the figure and this domain has been identified in many proteins involved in the complement system. Other aliases for this domain include short consensus repeats (SCRs) and the Sushi domain, from which the protein gets its name. The Fibronectin type III domain (FN3) is annotated in blue and the presence of this domain may suggest one of the properties of this protein as being involved in cell adhesion. SNED1 contains an RGD and a LDV sequence, important in the binding of other ECM proteins to integrins that are proteins found in cell membranes, an mediate cell-ECM interactions.

Post-translational modifications 13 N-glycosylation sites are predicted in the sequence of SNED1, and the presence of N-linked sites has been determined experimentally. SNED1 also has several predicted attachment sites for O-linked glycans and glycosaminoglycans, but these have not yet been validated experimentally at this time. There was only a few post-translational kinase dependant phosphorylation sites worth noting that resulted in a score of >0.8 by the NetPhosK program in the ExPASy Bioinformatics suite proteomics tools. These sites are annotated with yellow highlight in the conceptual translation above. All of these sites are predicted to be phosphorylated by either Protein kinase A (PKA) or Protein kinase C (PKC). Experimental evidence exists for phosphorylation at 12 residues: 5 serine, 5 threonine, and 2 tyrosine residues.

Secondary structure The amino acid sequence of the longest variant is incredibly cysteine rich, presumably resulting in a large amount of disulfide bond formation. The beta sheets are annotated as purple text in the conceptual translation and the alpha-helices are annotated as red text. The percentage of intrinsic disorder of processed human SNED1 (residues 25–1413) predicted by IUPred2A is 15.3%. A large proportion of random coil (73%) was predicted in SNED1 together with 26% of β-strands, and 1% of helix corresponding to a sequence found in the amino-terminal region of SNED1

… excerpt ends here. Continue reading the full article.

Worked examples

Example 1 — a first encounter with SNED1

Start with the simplest possible case. Write down what SNED1 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 SNED1 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 SNED1 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 SNED1

In research: SNED1 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 SNED1 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: SNED1 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Cysteine-rich proteins, Extracellular matrix proteins, Glycoproteins, so understanding it makes those chapters shorter.
In everyday life: Look for SNED1 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 SNED1 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SNED1 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 SNED1 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SNED1 in simple terms?

SNED1 (Sushi, Nidogen, and EGF-like Domains) is an extracellular matrix (ECM) protein expressed at low levels in a wide range of tissues. The gene encoding SNED1 is located in the human chromosome 2 at locus q37.3.

Why does SNED1 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 SNED1?

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 SNED1.