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

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2answers
17 views

Properties that can be derived from amino acid sequences [on hold]

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
votes
1answer
19 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 ...
0
votes
1answer
14 views

What is “chain identifier” in PDB?

The PDB file format is explained here. My question is what "chain identifier" is exactly? What is the difference between two residues which have the same sequence number but different chain ...
2
votes
1answer
73 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 ...
0
votes
0answers
24 views

What the definition of a flanking residue? [closed]

What the definition of a flanking residue? How do you define whether an amino acid is flanking or not? What are the environmental or physiochemical conditions in which a residue is considered to be ...
2
votes
2answers
29 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
votes
1answer
38 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 ...
1
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1answer
59 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 ...
0
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0answers
31 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?
1
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0answers
8 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 ...
1
vote
0answers
8 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 ...
8
votes
1answer
750 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
40 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 ...
1
vote
1answer
33 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?
1
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2answers
26 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
43 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
0answers
14 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 ...
10
votes
2answers
913 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 ...
-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 ...
1
vote
1answer
31 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
133 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
31 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
35 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. ...
1
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1answer
35 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, ...
2
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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 ...
5
votes
2answers
69 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
29 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
26 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
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1answer
27 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 ...
1
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1answer
35 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
86 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
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3answers
62 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
47 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) ...
3
votes
1answer
53 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
72 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
45 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 ...
0
votes
1answer
16 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
25 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
30 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
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0answers
25 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 ...
2
votes
1answer
29 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
36 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
136 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 ...
12
votes
2answers
115 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 ...
4
votes
2answers
124 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
40 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
32 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
47 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 ...