Questions tagged [proteins]

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

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Are Hsp70 proteins only activated in response to heat shock?

Hsp70 proteins are chaperones that assist in protein folding in my plant physiology textbook it says the Hsp70 proteins were discovered by inducing heat shock. But do they only work in response to ...
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Why is sickle cell trait expressed in half of all cells rather than all cells containing half-sickled haemoglobin

If sickle cell trait is due to be heterozygous with respect to a single gene mutation on the haemoglobin β-globin chain, why is it the case that ~50% of RBCs are sickled rather than half of the ...
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What is in the CIP and ethanol peaks following an IEX run?

I'm trying to separate lipid nanoparticles and protein impurities, and I keep getting low particle, A280, and A600 recoveries. Some "particles" and a lot of absorbance/turbidity come out in the final ...
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How to get a list of kinases that phosphorylated a particular protein?

I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue. I want to know which proteins could have ...
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62 views

What's a good reference for learning about recombinant proteins?

I'm looking for books and articles that can bring me up to speed on the design, expression, and purification of mammalian proteins in recombinant systems, both in E. coli and in more complex systems ...
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Is mucus significantly affected by the presence of ions?

In mucus, there is besides water and the mucins (Proteins for mucus), there are Ions like $Ca^{2+},Na^{+}$, etc. I have read that These Ions can Control the mucus swelling, i.e. the volume that the ...
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3answers
77 views

Are there any proteins not found in the brain that are affected by prions?

A prion is an abnormally folded protein that is capable of causing otherwise normal proteins to also misfold and become prions. They are responsible for causing diseases such as Kuru and Creutzfeldt–...
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Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a ...
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Protein folding

I've two questions 1. Is free ATP available in the cytoplasm of the cell? 2. In the protein folding funnel, prions and other misfolded proteins are located at the local minima of the graph. If ATP ...
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1answer
122 views

Can any one explain me the structural difference between Proteins and Peptides? [closed]

I have read in books that Proteins and Peptides are fundamental components of cells which carryout important biological functions.Can any one explain me the structural difference between Proteins and ...
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Do carrier proteins constantly open and close or do they only work when a substance binds to them?

What causes carrier proteins to change shape ? Do they need energy to change shape? If that is true, how are they involved in Facilitated diffusion ? By changing shape, do we always mean opens from ...
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Does active transport always mean movement against its concentration gradient?

Can active transport occur if/when a molecule is too big to pass through the membrane but is going down a concentration gradient ? And does it only occur through carrier proteins/pumps ?
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Which lipoprotein has the highest protein content?

I know that HDLs have the highest protein/lipid ratio but know that the HDLs are very small molecules too and I couldn’t find the exact answer for this question. I mean, by amounts which of these ...
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is consuming collagen actually good for skin/joint health? [duplicate]

A coworker of mine insists on drinking a very expensive collagen supplement for their skin health. It seems like a gimmick- Doesn't the digestive process breakdown proteins to their constituent amino ...
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2answers
54 views

How do mutations and protein synthesis link to cancer?

How do mutations and protein synthesis link to cancer? I know that a mutation in DNA can cause the triplet code on the mRNA to change so different amini acids are made and a different order means a ...
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Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
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Is it scientifically feasible to compare two samples of different sizes, while values in each sample are average numbers?

I want to compare result from my protein docking experiments to various protein structures of the same protein. I have two samples and in Sample 1, I have ...
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Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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Fluorescence assays to identify protein concentration without adding a large peptide sequence?

I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. ...
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4answers
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Why does protein folding not depend on the order in which it is synthesized?

I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that: Similarly, success in de novo protein design bears on the question I ...
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2answers
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Which proteins are most sensitive to electric fields?

Many Proteins have ionic charges that can attract each other (e.g. Formation of salt bridges) or repel each other. On the other Hand, Proteins are mostly immersed in water that screens most of the ...
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115 views

Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
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1answer
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Why spider's web don't burn when electricity touches it?

I saw and spider on it's web at an electrical cable and thinked: If the web is made of proteins, why dont burn. Sorry, the photo is dark because is night in Ecuador
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Formation of disulfide bonds in protein expressed after transduction

Say I transduce a nucleic acid sequence using a viral vector that encodes a protein having at least one disulfide linkage. For simplicity, let’s assume that there are only two cysteines in the protein ...
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What is the typical range of volumetric productivity and cell density in aerobic fermentor bioreactors for microes?

Im doing research on biomass production. Its hard to find data for this question. I need citations to calculate the production rate of microbial biomass in bioreactors (e.g aerated fermentator). ...
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Estimating diffusion constant of a protein based on number of amino acids

Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, ...
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Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

All humans have the same sort of proteins in our bodies. Take haemoglobin for example. Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations ...
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1answer
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How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

I have two datasets, from different sources, that I need to compare. The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
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60 views

Does the arrangement of amino acids in a protein matter for nutrition?

Let's say there are two diets, consisting of entirely different proteins. If you split up all of the proteins from one day of each diet, you'll get the same set of amino acids and the same count of ...
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The Collagen Triple Helix

In the amino acid sequence X-Hyp-Gly (where X can be any amino acid) of the triple helix can the Hyp residue be both hydroxyproline and hydroxylysine? In our textbook it says that the Hyp residue is ...
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Why is sorbitol used in buffers?

Many protocols in my lab use sorbitol in buffers. For instance, in co-immunoprecipitation, we include it at a final concentration of 200 mM in our lysis buffer. I'm not entirely sure why though. I ...
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what is the relation between protein domain and disease? [closed]

I am computer science student, and I am interested in bioinformatics. Thus, I am just at the beginning of learning some biology concepts. I am asking about the relation between protein domains and ...
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170 views

What are the secondary structure requirements for cell-penetrating peptides AKA protein transduction domains

Cell penetrating peptides. Cell penetrating peptides (CPPs) are a class of short amino acid sequences which are sufficient for crossing cell membranes and delivering themselves along with any ...
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Is the chitin in an insect's exoskeleton cross-linked?

This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states: The exuvia is made of cross-liked chitin, and will not decay. You don't need any special ...
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Is α-keratin a fully functional protein?

Is α-keratin before it coils with another polypeptide, makes chains, and build intermediate filaments a fully functional protein? I mean, is the single monomer of α-keratin a protein or does it have ...
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What inactivates pepsin in infants?

In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach. Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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1answer
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Lysozyme amino acid sequence: N-terminal extension

I looked up the amino acid sequence of lysozyme here: http://www.biology-pages.info/L/Lysozyme.html Then I crossed referenced that with the lysozyme sequence on UniProt: https://www.uniprot.org/...
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What is the function of spongin in sea sponges?

Sea sponges (Porifera) use different types of skeletons to support their structures. Some skeletons are built from minerals, some are built from proteins like spongin, and some use both. My question ...
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Can denatured GFP show fluorescence?

GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we ...
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1answer
889 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 ...
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Relationship between Communication Proteins and Gap Junctions

What is the relation between communication proteins and gap junctions? Do the communication proteins make up gap junctions or something?
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How exactly is casein digested?

I mean it seems first step is rennin or pepsin digestion in stomach - then what happens with remaining peptides? I am interested in the whole process from casein to amino acids. Is there brush border ...
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81 views

Preserved alpha complementation over evolutionary time?

Has the result of alpha-complementation ever happened via mutation through evolutionary time, and been preserved in modern day organisms? In other words, has a functional gene product ever been split ...
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How do organophosphates actually work?

The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine ...
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Can protein structure be determined by X-Ray Diffraction in a single image?

I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration ...
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What is the subcellular location of synthesis of non-essential amino-acids?

What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this? I thought the whole point of DNA is coding for how to ...
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How can I get the yield of my purified immunoglobulins?

In order to get the yield of IgY through a set of purification steps, what method can I use? Thanks in advice!
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How can I change my buffer system for protein purification?

I have a protein that I purified in PBS buffer, pH 7. I will do dialysis to remove salt and will then further purify the protein with ion exchange chromatography. I will need to use another buffer (...
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What buffer should I choose for IEX chromatography for purifying IgY

I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
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conversion of distance matrices to pdb/coordinates

I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...