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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33 views

How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?

Quoting Richard Feynman from Chapter 3 of his book Six Easy Pieces, when he talks about DNA: Attached to each sugar along the line, and linking the two chains together, are certain parts of cross-...
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Why do large, aromatic residues prefer beta-pleated sheets?

I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning ...
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Measuring the protein content using UV Vis

The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
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Why is it difficult to compare phosphorylation in proteins and peptides?

In a recent project, I wanted to find out in what way phosphorylation of certain peptides is influenced by a specific environmental cue. So in a published research article I came across a list which ...
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62 views

What makes a protein structure discernible?

In Lehninger's Principles of Biochemistry, Pg. 116 states that "parts of proteins lack discernable structure." What exactly makes this protein not readable? Is it the complexity of the shape ...
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Which condition is most likely to cause a buildup of materials in the lysosome?

Stated below, I must answer a question related to lysosomes. I am unsure of the answer, and have explained my reasoning after the question. Lysosomes contain hydrolytic enzymes that derive from the ...
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What are the stretch of amino acids?

I found the words "stretch of amino acids" in a newspaper article. "This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly." What is the &...
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Collagen, are fibrils arranged in overlapping fashion too just like tropocollagen?

Collagen molecules (tropocollagen) are interlinked into fibrils, with a banded structure showing the spaces ("lacunae") between the molecules. Do fibrils in turn also interlink in a similar ...
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Eukaryotic cell lysate-based protein expression efficiency

What is average efficiency of eukaryotic cell lysate-based protein expression systems in terms of (mg of protein expressed) / (mg of lysate) ?
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Questions about Cohesin - what does the ATPase domain do, and any suggested PDBs to look at?

I've been reading about cohesin lately, and I'm confused about the head subunit interactions. I've read a few papers, and also found this nice figure from wiki that demonstrates the crux of my ...
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What is the purpose of co-translational transport?

During intracellular proteins synthesis, all proteins are made by free ribosomes in the cytoplasm and some, but not all ribosomes (those which make membrane or secretory proteins) move to the ...
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How can Chronic myeloid Leukaemic drugs reduce the production of the Philadelphia genotype?

How can Chronic Myeloid Leukaemic drugs (Tyrosine kinase inhibitors, e.g. imatinib, etc.) that act by inhibiting bind of ATP to the active site of the BCR-ABL1 protein actually reduce the prevalence ...
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Does glycerol in E.coli culture media somehow inhibit the lac-operon?

I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
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Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?

Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?
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Is in the process of making soy protein isolate all (or most) of the protein trypsin inhibitor removed?

Being lactose intolerant and going to the gym I looked for lactose free protein powder. Soy protein isolate seemed like a good option until I read something about the protein Trypsin Inhibitor (TI). ...
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Determine similarity in percentages between species A and B, A and C, and B and C

The chart above is a graphic that shows the amino acid sequence differences between different organisms for a protein keratin. The question I am required to answer begins as, "Keratin is made up ...
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Can any molecule become a hapten?

Hapten are small-molecules, that can only become immunogenic when conjugated with a carrier protein. I was wondering if all small-molecules can become haptens (eg. by synthetic conjugation). Given ...
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What is meant by [protein name]+/- (ie “Myod+” and “Myod-”)

I have read a paper where this notation for protein names is used: Myod+ and Myod- (or another example, Myog+, Myog-). What does this indicate? In the paper I'm reading, and some brief googling, it ...
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Do voltage-gated channels in a neuron use ATP

I have a question about action potentials in a neuron. Do voltage-gated sodium and potassium channels use ATP? I mean when they are closed or when they want to open the gate, do they use ATP?
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Who discovered DNase?

I was recently studying genetics in which DNase had a crucial role in proving DNA to be the genetic material and I tried to find who discovered DNase (like the discoverer of DNA) but in vain. Who ...
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What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to align structurally different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, does that means the ...
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Howthe body differentiate between foreign and native protein? How does it know when to create an immune response? [duplicate]

How the body differentiate between a foreign and a native protein? Suppose there is a bacteria, it has lot's protein on its membrane, with specific structures. How does our body know it's the foreign ...
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What's superposition and thread in RosettaCM?

I'm a beginner in structural biology. I had a question while reading a paper on RosettaCM. What does RosettaCM's superposition and thread mean? I googled it. As a result, the following results were ...
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PDB id to protein environment ph [closed]

How can one find the information of a protein environment ph from its PDB id? Can one assume the ph to be the same as its cellular location?
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Why are some protein sequences known but their 3D structure isn't?

Why are there some proteins that have a known amino acid sequence, but their 3D structure is not known? Wouldn't finding the former in a lab lead to the discovery of the latter? Please correct me if I ...
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Does my reasoning about the first emergence of proteins make any sense?

In order to make proteins, a cell uses ribosomes, which itself is a structure made out of proteins. The first ribosome couldn't have been created with the help of ribosomes though, as the ribosomes ...
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What is the best way to find which domains in a list of InterPro IDs are catalytic?

What is the best way to find which domains in a list of InterPro IDs are catalytic? (In this case, we are looking at human enzymes and their domains' InterPro IDs.) Thanks in advance! Setz
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What is a Protein contact map, and how do I read one?

Protein contact maps are symmetrical and look great, but how does one read one? I tried to underside the following source: 'Understanding contact patterns of protein structures from protein contact ...
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How can protein allergens be passed from mother to baby via breastmilk is proteins are broken down after ingestion?

All over the Internet new mothers are urged to avoid dairy products, a slew of vegetables and even beef if their child displays symptoms of reflux. In the case of dairy, for instance, it is said that ...
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How do anticholinesterase pesticides kill nematodes?

Compounds that inhibit the enzyme acetylcholinesterase are commonly used as pesticides. In animals with centralized respiratory systems controlled by the nervous system, poisoning with an ...
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How are proteins containing other elements encoded?

If I understand correctly, proteins are formed by associating each three-letter DNA sequence to a certain amino acid. Yet there seem to be proteins which contain elements such as copper, which isn't ...
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Is this basic gene diagram correctly labeled?

I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what ...
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Why do nattokinase and serratiopeptidase remain effective when given orally, but not insulin?

Why do nattokinase and serratiopeptidase not break down in the stomach and intestines? Article says that serratiopeptidase is absorbed in rats intestines after oral intake - https://iubmb....
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Do people with higher body hair growth (eg. Women with hirutism) need more protein? [closed]

Hair is protein. Does that mean that the body of a woman with hirutism is using more than usual protein to make hair and thus she needs more for building and repairing muscles?
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Protein structure prediction from amino acids sequence

Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict ...
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A balanced diet with the minimum carbon footprint [closed]

Many studies shows that 1 kg of non-vegetarian food as 3-4 times more carbon footprint than 1 kg of vegetarian food. I think that does not represent the complete picture food from animal sources are ...
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How many proteins could participate in a complex

Disclaimer: I’m a computer science student with minimum knowledge of biology. I’m working on an algorithm to cluster proteins in Protein-Protein-Interaction Networks to find protein-complexes. While ...
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Available Protein sequence alignment dataset and HMM model

I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to generate noisy copies of the consensus sequence ...
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1answer
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Are there any proteins assembled from non-adjacent parts of the genome?

Many proteins are assembled from multiple exons with the introns between adjacent exons being spliced out. But are there any proteins that have unrelated to them exons in the middle of their sequence? ...
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Meaning of “Domain with function to find” (FIIND)

From NALPs: a novel protein family involved in inflammation. FIIND - Domain with Function to Find. What is the meaning of this name? Does it mean "Domain with an unknown function"? I'm ...
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Can DNA be used directly to determine the age of a mutation?

I've studied that proteins found in a sample as biochemical evidences for evolution. Its variation in structure and configuration can be used to date the age when that mutation occured, effectively ...
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single nucleotide polymorphism and protein domain

I have a list of nsSNPs (e.g. rs121918549) and I want to know what are the protein domains that contain those nsSNPs. Can someone suggest a way to do so (some online database/tool)? Thanks in advance
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What's the role of bromelain in pineapple?

Bromelain refers to one of two proteases found in pineapple and its relatives. Like other proteases, many believe it has therapeutic uses and it's the subject of a lot of research. But what role does ...
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network with all the interactions of the alpha-synuclein protein

I would like to make a network with all the interactions of the alpha-synuclein protein (in homo sapiens), that is, I would like to visualize the pathways where this protein participates, I would also ...
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Glycocylation or glycosylation?

I came across a few sources that refer to glycocylation. Is this the same as glycosylation? See for instance page 237, or the abstract in this paper. ...
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Type VII collagen binds type IV collagen?

What are the functions of type VII collagen ? My book says it 'binds type IV collagen', does that just mean it binds type IV collagens together to form a sheet or a network of type IV collagen for ...
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Why don't carrier proteins require energy to change shape?

I know that carrier proteins can be used for both passive and active transport, but I am referring to the facilitated diffusion aspect. Even though facilitated diffusion via carrier protein goes along ...
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How to filter the PBD databank for “single-domain proteins with full length 3D-structures solved”

I am trying to reproduce a machine learning model that has been developed here. As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a ...
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Need either a [similar] ribosome to the following few | a heuristic for finding [similar] macromolecule given 20 others

Background : Hi! I am running a small experiment dealing with structural heterogeneity of the ribosome, actually of ribosomes across all domains of life. It's entirely computational: I get cryoEM ...
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How much of the genotype-phenotype map do we understand in HIV?

From what I understand, viruses have very small genomes relative to those of standard model organisms used in biological research. For example, according to Wikipedia, "the HIV genome contains nine ...

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