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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How are DNA polymerase error rates measured?
It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
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Rosetta ab initio prediction and protein-protein interaction fitness help [closed]
I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to ...
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Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?
I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as ...
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Determining if a Protein Model Contains a Backbone Clash
I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be ...
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Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?
I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express.
Depending on the ...
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Exactly which amino acids are phosphorylated in higher plants during state transitions?
I know it is usually stated as the threonine residue near the N-terminus of either light harvesting complex (lhc) b1 or lhcb2, but if this is somehow lost, say in a mutant, is the system flexible ...
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How would I explain different properties of the same protein in different species?
I recently finished an experiment where I analyzed the rate of ATP hydrolysis of Heat shock protein 104 in three species of fungi. They have shown to all have different rates of ATPase activity. How ...
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Macromolecule levels in daughter cells after fission
When a prokaryote undergoes binary fission, how are the non-DNA macromolecules distributed between the two daughter cells? This is motivated by comments on a previous question and a G+ discussion. I ...
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How to compute properties of peptides ?
I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :
Length of ...
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What role does a protein's size have on protein-protein interactions?
Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
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How does Yeast-two-hybrid detect interactions between several proteins in one experiment?
I am trying to understand the Y2H screening method. I can understand how we can check if two specific proteins interact with each other. For example, if we want to check whether protein A and protein ...
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JMol "calculate HBONDS": which atom is the donor/acceptor?
JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds.
Here's one line from an example ...
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Can two protein secondary structures "overlap" in the PDB?
I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:
...
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Calculating Protein Concentration from Kilo Units (KU)
I am looking to purchase Pyruvate Kinase from the Sigma Website, they state the volume in Kilo Units (KU) i.e. 1, 5 or 25 KU. It also states there are 350-600 units / mg protein.
Does this mean one ...
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How are proteins formed?
Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?
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How do proteins and genes participate in learning?
I am a computer scientist that studies biology and bioinformatics.
In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and ...
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How does protein help to cure wound? [closed]
I understand that the protein helps to repair body tissues. If I increase the intake of protein, would it help to cure the wound more quickly? I would like to know how does the protein reaches the ...
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Two subunits connected by only one disulfide bridge: quaternary structure?
I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides ...
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Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?
What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?
If none are known, what computational tools might be used to search for such examples?
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Which concentration of BSA is recommended for dynamic light scattering experiments?
What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ?
I ...
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How can I predict DNA binding affinities from a protein sequence?
Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?
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Are Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70 positively charged or negatively charged? [closed]
Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70,are they
positively charged or negatively charged ? And which other solvents can be used as a substitute to water for preparing solutions in each ...
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Are quaternary protein monomers unique to a particular protein complex?
I know that quaternary protein structures are formed exclusively via non-covalent bonds. My biochemistry professor discussed a viral capsid that is essentially one quaternary structure with 240 ...
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Do gene expression levels necessarily correspond to levels of protein activation?
I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid?
My problem ...
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Protein construct design
I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying start/...
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Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?
I'm talking about this type of post-translational modifications. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature ...
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What's the opposite of a thermophile?
Thermophiles, heat-loving organisms, have been a popular topic of research for decades due in large part to the utility of their enzymes in various chemical reactions (Taq Pol single-enzymedly made ...
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What is the significance and method behind Ramachandran plots?
My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and ...
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Protein Biology Cheat Sheet
I'm looking find a cheat sheet for protein biology to stick on my desk to remind of some of the key principles of protein biology. I seem to remember the specific and complex principles in protein ...
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What are the various types of protein-protein interactions
I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?
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What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?
I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an ...
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Is there a binding affinity metric for interactions not in equilibria?
I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the ...
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Can any protein be phosphorylated?
I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (Skowrya et al., 1997). I have heard of ...
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What are the most important differences between HSP70 and HSP90?
Question originally asked on Quora. These proteins have many functional similarities, so why do cells need both to handle unfolded proteins?
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PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?
I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
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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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How does the enzyme ATP Synthase use a proton concentration gradient to make ATP?
I understand what the enzyme ATP synthase does, but I'm not exactly sure how it does it. I've heard that it uses rotary catalysis, but how exactly does this work? How is the energy from the H+ ion ...
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Is the protein in teardrops still attached to cells, or is it released and free-flowing?
A ScienceDaily article says that the protein in teardrops can kill bacteria.
But how does it reach the bacteria?
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How many human proteins are very well characterized?
Following up on How many human proteins have a solved 3D structure?,is there a list of very well characterized human proteins / protein complexes?
My criteria for "very well characterized" includes,...
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When does oxidation destroy prions?
It seems like a no-brainer than oxidation, playing the, er, role it does in the universe, would destroy prions just like it destroys everything else.
But when does it do that? I assume this has been ...
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Intrinsically disordered proteins as potential drug targets
Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological functions....
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What effect has changing pH and salt concentration on protein complexes?
I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...
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Why are restriction enzymes not frozen?
We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is ...
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How many human proteins have a solved 3D structure?
I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
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