Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

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2
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1answer
19 views

Do the enzymes and compounds in saliva help with stain removal?

Does spitting on stains help with removal? Saliva is high in amylase that should help with the breakdown of protein rich stains like blood and semen. It also contains antimicrobial enzymes and ...
0
votes
1answer
22 views

How does the structure of the pancreatic acinar cell relates to its function?

So the pancreatic acinar cell synthesizes, stores and secretes digestive enzyme precursors called zymogens e.g. pepsinogen. The structure of the acinar cell shows that there is an apical and basal ...
10
votes
2answers
894 views

Why and how does uniprot list ~150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns ~146,000 proteins. I was under the impression that there were only 20-25,000 proteins in ...
0
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0answers
11 views

How are membrane and extracellular proteins delivered to the target membrane?

In bacteria, either folded or unfolded proteins can be trafficked to the membrane or the extracellular space provided that they have the appropriate signal sequences. Once the chaperones or Signal ...
-3
votes
1answer
34 views

Phosphorylation capacity of an enzyme [closed]

Let's think ProteinA can phosphorylate proteinB, proteinC and proteinD. Condition1: All proteins are expressed and proteinA phosphorylates proteinB, proteinC and proteinD. Condition2: Only proteinA ...
7
votes
2answers
119 views

What are some (bioinformatic) methods to characterize potentially novel gene transcripts?

I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, ...
0
votes
1answer
23 views

How does the MET gene work and what happens when the promoter region gets mutated?

I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET ...
4
votes
1answer
138 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
1
vote
1answer
33 views

Can Nanodiscs be used to study membrane energetics?

Nanodiscs have changed they way we can study the structures, insertion, and functions of transmembrane proteins. Below is an image of a nanodisc bilayer. The key difference, as far as I can tell, ...
12
votes
2answers
102 views

How can we verify predictions of protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
0
votes
1answer
30 views

How reliable is SwissProt topology?

I am using TOPO_DOM annotations from uniprot databases to characterise the orientation of transmembrane features. Is SwissProt topology experimentally validated, ...
0
votes
1answer
33 views

What is the difference between options protein and replication in the NCBI database?

After checking the NCBI help page, I am still unclear about the difference between protein and replication interactions for HIV. ...
5
votes
2answers
39 views

Need some good resources to learn about Protein function and structure

I'm taking a course on biochemistry at edx. Since I'm a computer science student, I'm having some trouble in understanding many biochemical concepts. While the first module was just fine, I found the ...
4
votes
1answer
27 views

Which hydrophobicity scales are best for detecting transmembrane regions, and why?

There are many hydrophobicity scales for protein analysis. Broadly, I gather the differences between them are from the experimental method to acquire the data and the normalisation (or lack thereof) ...
2
votes
0answers
14 views

What is internal symmetry in membrane proteins?

I have come across the term "internal symmetry" in the context of membrane proteins, but have never found a satisfactory definition. I'm struggling to figure out exactly what this term means... What ...
3
votes
1answer
222 views

How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
2
votes
0answers
24 views

What are all of the currently known variations of the G zipper motif?

The G zipper motif is found in transmembrane proteins at an above random frequency and there are models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly. ...
1
vote
1answer
31 views

Why cooked food considered nutritious if proteins decompose at much lower temperatures?

Food is cooked/baked at temperatures that are significantly higher than what's considered normal for proteins/amino acids (40°C). Then why such food is still considered nutritious after cooking? ...
7
votes
0answers
66 views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
1
vote
3answers
58 views

LCMS/MS versus Western Blot

I have a general question regarding which method would you recommend me to use if I would like to investigate the difference in the level of several proteins in tissue samples and compare different ...
-1
votes
3answers
43 views

Patterns/Motifs Repository [closed]

I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching). I am curious about the "regular expression (regex)" (pattern/motif) ...
7
votes
1answer
92 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
2
votes
1answer
41 views

How is the subunit molecular weight different from the native molecular weight?

I noticed that the native molecular weight for an enzyme is different from its subunit molecular weight. Why are they different? Aren't the genes needed to express the enzyme the same in the native ...
2
votes
1answer
69 views

Consequence of Plants as Incomplete Protein Source

Some years ago, in a 1000~ level biology course we learned that the DNA essentially encodes formulas for creating proteins from amino acids. While the human body can synthesize many many amino acids, ...
4
votes
1answer
39 views

Why do some protocols require prewarming a liquid medium before inoculating?

For example, in this protocol for E. coli competent cell preparation, it says: Plate 10 uL E. coli BL21(DE3) cells on a LB-agar plate; incubate overnight (12 hours). Prepare 500 mL SOB medium ...
2
votes
2answers
39 views

How does a cell create/gain its initial ribosomes for protein synthesis?

I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes ...
0
votes
1answer
15 views

Will tagging a protease with HlyA for secretion inactivate the protease?

We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli ...
4
votes
1answer
24 views

Proline Iminopeptidase v Proline Aminopeptidase

We're an undergraduate independent research team and we are having trouble purchasing commercial proline iminopeptidase as it is unavailable on Sigma Aldrich and very expensive on other websites. We ...
1
vote
0answers
21 views

aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel. I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about ...
0
votes
0answers
16 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
9
votes
1answer
148 views

Circular mRNA to produce long proteins

Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I ...
2
votes
1answer
26 views

In protein-protein interactions what is the difference between a binding site and an interface?

I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?
1
vote
2answers
26 views

T7 Tagging Next to Met

Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence? Thank you!
2
votes
1answer
31 views

Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?

As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to ...
2
votes
0answers
51 views

What effects would be caused by exposure to common life forms with opposite enantiomer biology? [closed]

Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything. What would the effects be of that human's ...
7
votes
1answer
120 views

What is peptide mapping?

After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand ...
5
votes
4answers
122 views

Any good website/book to understand protein folding and enzymes?

I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. I understand that the protein is a polypeptidic ...
4
votes
3answers
91 views

Amino acid compatibility

The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH2) that can potentially form a peptide bond. ...
6
votes
2answers
526 views

Solvent Accessibility, the 20% cut-off method

I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value. I understand how the RSA is ...
4
votes
2answers
112 views

Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
0
votes
1answer
28 views

Using Jpred to predict secondary structure

I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i ...
0
votes
1answer
28 views

One Gene and many proteins [closed]

Imagine a gene with $n$ exons and $m$ introns. How many proteins are possible from that gene? Would all the proteins be isoforms?
1
vote
1answer
44 views

Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved?

Why are some protein complexes composed of many different types of proteins? How many different types are they composed of? In particular, which protein complex has the greater number of different ...
3
votes
1answer
60 views

Why do some proteins “use” a beta barrel structure instead of alpha helices in transmembrane space?

Most proteins are fixed in the membrane by alpha helices. But some use beta barrels. Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil ...
4
votes
1answer
29 views

Are all protein composed of all the amino acid (in animal) or are there less diverse protein?

I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ...
5
votes
2answers
1k views

What has caused life to choose this unfathomably tiny subset of all possible proteins?

I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ...
14
votes
4answers
950 views

How many human proteins have a solved 3D structure?

I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
6
votes
2answers
344 views

What is the purpose of using two layers of gel in SDS- PAGE?

I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about ...
0
votes
1answer
43 views

What is a complex?

In my text book it says that "Troponin" is a complex of Troponin C, I and T. In this sense, what is the relation between Troponin complex and C, I, T?
0
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0answers
45 views

Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...