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

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How to recognize a conserved motifs of the protein

I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids ...
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50 views

Formation of peptide bond..?

Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by ...
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32 views

What does the term 'modified residue position' in phosphorylation mean?

Does it mean the position of the amino acid in the protein sequence, or something else? For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the ...
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Which point mutations in proteins are OK, and which cause significant change?

I heard that some point mutations in proteins are OK, like from alanine to glycine (I'm not sure, it's just an example), some will change the protein significantly. I want to understand deeper but ...
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117 views

What Proteins Are Universal To All Life Forms?

According to National Geographic, there are 23 proteins that are common to all life forms: All species in all three domains share 23 universal proteins, though the proteins' DNA ...
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69 views

What I can do in order to improve the folding of the protein?

I am struggling with the expression of the certain protein. It seems that it is not properly folded and thus, it is not active. I tried to express it at the lower temperature and for the longer time, ...
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65 views

level of organisation of proteins

Is there any disulphide bond in a quaternary structured protein? If yes, please provide examples. In tertiary structured proteins, what is(are) the most important characteristic(s) of tertiary ...
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2answers
98 views

What are the naming conventions for mutations of proteins?

I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50. Please can someone explain the ...
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104 views

alpha tubulin molecular weight problem

Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.
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Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
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1answer
29 views

How are cyclic hormones characterized?

I have a question regarding the description of a subset of peptide hormones, called cyclic hormones. Two examples of cyclic hormones would be somatostatin and melanin-concentrating hormones. I know ...
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1answer
154 views

What do the Clustal Alignment Symbols Mean?

Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?
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358 views

Why digest proteins into peptides for Liquid Chromatography - Mass Spectrometry?

Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is ...
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109 views

Color van der waals bonds in swiss PdbViewer

I'm trying to color certain amino acid's van der waals bonds as in the following picture: can anybody please describe the steps to accomplish that?
3
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41 views

The use of proteins in memory creation

I have very limited knowledge of how the human memory works as I think, at this time, most people do. However, I have been reading and some articles which say, and I quote the article just linked ...
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1answer
56 views

Curious about Brazzein

What is in compound "Brazzein" that it makes it 2000 times more sweeter than sugar? Can anyone please explain the science behind it?
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2answers
229 views

What are the functions of disulphide bonds?

What are the functions of disulphide bonds between amino acids in proteins or peptides?
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1answer
41 views

conservation of C-peptide sequence in the guinea pig

Where can I compare the C-peptide sequence of guinea pig with human or mouse? I am also interested in finding whether the guinea pig has insulin 1 and 2 to know whether I could use an anti-C-peptide 1 ...
2
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1answer
354 views

What is optical density in Lowry's protein estimation method?

I have a few questions: What is an OD value? Why do we use blank solution in Lowry's protein estimation method? If The OD of a protein is 0.01, what does it mean? Thanks in advance.
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13 views

To decrease the amount of proteins in the lymphatic drainage for short term

I am looking for some mechanism which can decrease the amount of proteins in the lymphatic drainage only for short term. Assume there is no flow between capillaries and lymphatic system because the ...
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1answer
26 views

fibrinogens and fibrins - are they the same molecule?

Some proteins are "activated", like fibrinogens; they are turned into fibrins by thrombins, and then the fibrins can aid in blood clotting. Are fibrinogens and fibrins the same molecule, just in ...
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881 views

Is there a protein in the eye that gets kinked by photons and shipped down to the liver to get un-kinked?

My friend made the claim that there exists a protein in your eye responsible for vision. This protein is sensitive to different wavelengths of light, and when it gets hit by the right wavelength, it ...
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1answer
2k views

Why do three nucleotides code for one amino acid? Why not 5 nucleotides? [duplicate]

We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon?
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Can protein precipitate out in alcohol during DNA extraction?

In common lab sessions to extract DNA from strawberry or cheek cells, will there be protein contaminating the DNA extract in alcohol? If so, how can we prevent protein from precipitating out of the ...
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1answer
36 views

Protein Conformation Modeling

I'm interested in learning about computational modeling in biophysics. I have heard some amount about people modeling proteins as a network of ideal springs to examine things like conformation ...
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77 views

Function of heparin and dextran sulfate for removing proteins

From this article : The reaction was terminated and the histones, and most nonhistones, were removed by adding the nuclease-treated chromosomes to a solution containing dextran sulfate (2 ...
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1answer
428 views

What can cause the bloating in high protein diet of Whey proteins?

I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), ...
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1answer
38 views

If a gene altered causes cancer and creates a protein for cancer can the new protein be isolated in some way?

In the above title question, can the protein thats altered not be isolated (to separate out from other proteins) somehow? Is there nothing that can bind to the specific cancer proteins that will not ...
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1answer
122 views

how do they identify different protein chains?

Can someone please explain how different protein chains occur exactly? I'm not talking about the side chain, but the protein chain which is typically labelled as A,B,C etc in the PDB. I'm curious as ...
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36 views

Evolutionary rationale behind migration proteins

Tumor cells are able to migrate due to specific migration proteins. What is their evolutionary origin? Or are they simply deregulated?
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166 views

pI and pH relationship in context of ion exchange protein purification

I am confused about relationship between isoelectric point and pH in context of ion exchange protein purification. Why we cannot use this method for protein with pI below 7? Thank you very much for ...
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106 views

Conserved proteins are non immunogenic

I read that proteins that have been highly conserved are non-immunogenic. Why is it so ? What is the special thing that makes it non immunogenic(antibodies against them are hard to make) ?
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What happen's to a virus's capsid after it injects its genetic material into the host cell?

After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it ...
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121 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 ...
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1answer
78 views

Length differences between physically interacting proteins

What can be said on the length differences between interacting proteins? Are they usually of similar sequence lengths or not at all?
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51 views

Ferredoxin synthesis pathways

I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of ...
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How to parse SCOP parseable files PDB residue identifiers?

I am trying to parse the SCOP parseable files, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the ...
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1answer
46 views

Does Sirtuin protein family Sir2 work in low-calorie diet mostly?

I am reading about the protein family in relation to the prolongation of cell life. It is known that Sirtuins have been implicated in influencing a wide range of cellular processes like ageing, ...
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1answer
35 views

Staphylococcus AG structure?

I found this statement in my study materials in the section of Staphylococcus The AG structure: protein AG (species specific); polysaccharide AG (serotype specific). I know what is ...
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40 views

Vesicular and non vesicular transport

I have to classify them either as transported in vesicles or without vesicles. What I think - Non-vesicular 2.vesicular 3.vesicular 4.vesicular 5.non-vesicular 6.vesicular 7.vesicular ...
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Why are genes expressed as proteins rather than other types of bio-molecules?

I guess, we could infer that the structure of an amino acid has the same functional units as RNA is used to synthesise it. Therefore, from a logical point of view it would make sense that genes are ...
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82 views

Topology of protein

The domain structure of protein Z, which is composed of 180 amino acids, is shown in the upper part of the figure below. Protein Z is palmitoylated at a cysteine residue (the third amino acid) ...
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1answer
51 views

Epistasis when interacting loci are codons within a single gene

There is epistasis when the effect on the phenotype of one gene is influenced by one or more other genes (called modifiers). Is there a similar concept when the effect on the phenotype of one site ...
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1answer
189 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...
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1answer
163 views

What type of mutation causes Progeria?

I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease. I know that the LMNA gene codes for the "prelamin A" protein, and that protein contains ...
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Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA [closed]

We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The ...
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3answers
190 views

What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
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Removing Sugars Bound to a Protein

I recently purchased some Maltose Binding Protein and as the name suggests this protein binds to maltose. The problem I have is the protein arrive with maltose bound. I know this through native mass ...