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

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Determine secondary structure (per residue pair) from a protein contact map

Given a protein map contact map (which for this particular case is a matrix of all Ca-Ca atoms in protein 1a3a that are less than 8 Angstroms): Question: For ...
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2answers
61 views

yeast protein secondary structure

i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous ...
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37 views

Wash adsorbed protein without destroying Biotin-Avidin-Mechanism

I am looking for reliable protocols to wash protein (e.g. Fibronectin) adsorbed onto glass surfaces. According to Protein immobilization literature, people usually use 1% SDS and some incubation time. ...
3
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1answer
93 views

What is the shortest mRNA the ribosome can read to produce a peptide?

This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome. In general, Glutathione has a "gamma" ...
3
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0answers
63 views

Relative densitometry from SDS PAGE

I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software. My questions are ...
5
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2answers
147 views

Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome?

Case: I am writing a summary for a class in protein structure and function, and was asked to describe some different ways that peptides are synthesized (that does not involve the ribosome). I ...
2
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1answer
60 views

Difference between the P4 and P5 subtypes of P-type ATPases in plants

In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?
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26 views

How do molecular recognition features work?

The occurrence of relatively short (10–70 residues), loosely structured protein regions bind within longer, largely disordered sequences that were characterized as bound to larger proteins. These ...
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23 views

Effects of Acids and Bases on protozoa

Why is it that when you pour acid (HCl) on a culture of Euglena gracilis in an aqueous environment the protozoa begins to swell and when you pour a base (NaOH), it maintains its shape? I feel like ...
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30 views

Why would the addition of whey protein to oatmeal make the oatmeal more runny?

So, at the suggestion of a friend I added some protein to my morning oatmeal. While I do feel better for it, I noticed a few things it did to the oatmeal I didn't expect, the primary is that the ...
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1answer
112 views

How protein denaturation affects digestion?

Which one of these is a) easier to digest, b) more nutritious (in whatever sense): 1. scrambled egg, 2. raw egg. Bascially is "denatured protein are worse than not denatured" a myth, or not?
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78 views

How is the volume of the dialysis buffer decided?

Is there a specific ratio between the volume of enzyme solution in semipermeable membrane bag and the volume of the buffer outside the membrane bag? I have been looking for a specific formula or ...
0
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1answer
19 views

C-myc/anti-myc Ab Interaction with Fusion Proteins

I am going to prepare a c-myc fusion protein with the following configuration: (28-residue signal sequence)-(c-myc)-(GGSGGGSG Linker)-(Protein of Interest (POI)) POI is a transmembrane protein and ...
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0answers
47 views

Protein modification and ATP consumption

According to wikipedia there exists a lot of ways to modify a protein (post-translationally). Just to mention few: phosphorylation, dephosphorylation, glycosylation... While phosphorylation requires ...
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1answer
50 views

What are the key differences in giant and large unilamellar vesicle preparation processes?

I have to study my peptide's folding on membrane mimetic (model membrane) by circular dichroism spectra. Now I'm looking for suitable methods for preparation of vesicles: LUV, SUV, GUV- large, small ...
3
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2answers
90 views

What signals a ribosome to stop production when the cell is out of available amino acids?

In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of ...
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47 views

Question about Collagen and Glycosylation

Just curious, I know that collagen typically undergoes O type glycosylation. However, can you say that this type of glycosylation is essentially like putting a mailing address for proteins to be ...
2
votes
1answer
44 views

Do residue sequence numbers in PDB files correspond to the positions in the backbone?

In other words if two residues have sequence numbers, say, 20 and 21 then are they next to each other in the backbone? If no (or not necessarily) then is there any way to find consecutive residues ...
3
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1answer
111 views

Difficulty in finding protein inhibition drugs

I was reading an article on a recent identification of a PARP-14 protein in cancer cells that is responsible for production of additional glucose which keeps cancer cells from dying, and that a PARP-...
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1answer
54 views

Molecular weight of my 2-D gel

I am a little confuse when I try to figure out the molecular weight of the marker on my gel. I used NuPage Novex 4-12% bis-tris gel and Mark12™ Unstained Standard as a marker. Could please someone ...
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46 views

Western blot extrange band

I performed a WB using plasma rats and monkeys samples with anti ubiquitin K-48 antibody. In every sample the antibody binds something and it appears a specific band that seems to be 71kDa. When I ...
4
votes
1answer
338 views

How can a polar molecule pass through polar channels of proteins in the cell membrane?

To transport a polar molecule through the nonpolar cell membrane, a protein with a polar channel is needed to allow it to diffuse. However, if the molecule is polar and the channel is polar, wouldn't ...
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1answer
88 views

What is a detailed chemical explanation for describing how an enzyme may lower the activation energy of a reaction?

If you can provide some sound reasoning that touches on tertiary structures of proteins and does not use a lot of advanced chemistry jargon that might be really helpful, especially for an intro ...
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1answer
285 views

How do DNA-binding proteins determine that they're binding to the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
2
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3answers
575 views

Amplification technique for proteins similar to PCR for DNA?

I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up ...
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0answers
30 views

Consumption of different type of energy when one is inactive

I'm wonder if there is any study done on this and what are the results? how much of each type of energy one's body(healthy normal person) uses when inactive(seating down) I know there are alot of ...
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2answers
49 views

Properties that can be derived from amino acid sequences [closed]

What are the properties that can be derived from an amino acid sequence apart from those mentioned in the website? In the mentioned website, the properties that can be calculated from amino acid ...
3
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1answer
264 views

What is the significance in an alpha-helix being right-handed or left-handed?

Why is that often when alpha-helices are discussed, it is also mentioned their direction - right-handed (clockwise) or left-handed (anti-clockwise)? I have heard that left-handed alpha-helices are ...
2
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1answer
119 views

Are all dipeptides synthesizable?

Probably a basic question, but are all possible dipeptides synthesizable? For 20 amino acids, there should be in principle 190 dipeptides; do they all exist or is there chemistry that makes some ...
2
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2answers
60 views

Are multi-chain proteins synthesized as one biological unit?

Are multi-chain proteins (especially homo/hetero-dimers) synthesized together as one overall unit or are they separate monomers which bind together at some point after synthesis, and are there any ...
2
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1answer
93 views

Why are VAL, MET and ALA substitutions commonly used for protein behaviour and function studies?

I have seen that amino acids are commonly replaced with VAL, MET or ALA to study the effects of these specific substitutions. Why are these specific amino acids used in particular, what are the ...
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1answer
572 views

Doubts regarding definition of upstream/downstream genes and cognate protein

With respect to the research paper, there are a few things I didn't understand: 1. What is upstream and downstream gene 2. This paper identifies proteins that help in secretion, but does not identify ...
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52 views

Proteins and Blood Acidification

Is there evidence to suggest that excessive consumption of Whey, or similar proteins will lead to acidification of the blood?
2
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17 views

Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
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16 views

How are split inteins joined?

Do they form a peptide bond? Or is it just some affinity/van der Waals interaction? Is the mechanism enzyme catalized? Are the residues/moieties at the join site known? Could they be introduced to ...
10
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1answer
775 views

Did not understand a small excerpt from a research paper

Was going through this paper, among multiple things that i did not understand, I came across this part: Each amino acid residue of a single window was encoded into a unitary bit string of length ...
2
votes
0answers
103 views

Multiple transcripts encoding for one protein

Trying to get a better understanding of the process of DNA to proteins. So when we have a gene, it is read from the 5' to 3' end, only translating the exons to mRNAs. A single gene can have multiple ...
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1answer
245 views

Gene and Protein isoform

What is the relationship between term "Gene isoform" and "Protein isoform"? Say a gene can make 3 isoforms, will it produce only (maximum) 3 isoform protein?
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2answers
41 views

Protein that exit from the cell - as marker

Searching for some protein, that I could use as extracellular marker for mammalian cells. I need to insert mRNA to cell, and to detect the protein outside the cell (not on membrane) if the mRNA ...
2
votes
1answer
376 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
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0answers
69 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 ...
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2answers
1k views

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

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
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1answer
43 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 ...
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1answer
50 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 ...
7
votes
2answers
229 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
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1answer
38 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. http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/...
2
votes
1answer
90 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, ...
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1answer
41 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 ...
5
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2answers
189 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 ...
3
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1answer
45 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) ...