Questions tagged [protein-structure]
The 3-dimensional organisation of amino acids in a protein, specifically including the secondary, tertiary and quaternary structures.
158
questions
3
votes
1answer
87 views
What other sites do non-competitive inhibitors bind to apart from allosteric sites?
I learned competitive inhibition and non-competitive inhibition.
My teacher told me that we should say that non-competitive inhibitors bind to somewhere on the enzyme apart from active sites.
I ...
5
votes
3answers
297 views
Why are there so few full-length antibody structures?
I’m a student in the Biochemical Engineering field and the professor at the department just told us in a lecture that if we want to use a full-antibody structure for simulation purposes there aren’t ...
0
votes
0answers
68 views
What does 'disordered' mean in the 'Family & Domains' section of UniProt?
I am looking at information about a protein called CD83 antigen on UniProt. On the page for the protein, in the 'Family & Domains' section, it says that between amino acids 60-81, the region is '...
0
votes
0answers
35 views
Determine directionality of backbone from electron density map
I am given a polypeptide with three electron density maps at different resolutions; 1.85, 2.5 and 3.5Å. And from this I am to determine at which resolution you could be certain about the ...
0
votes
0answers
26 views
Is there a reationship between fiberous and globular nature of protein and the polarity and hydrophobicity/philicity of the constituent amino acids?
My question is based on the following resources that I was looking at:
https://lab.concord.org/embeddable.html#interactives/interactions/protein-folding-exploring.json
https://authoring.concord.org/...
-1
votes
1answer
120 views
Could p-loop bind fully protonated ATP?
The phosphate tail of ATP binds the p-loop motif, evolutionary conserved, going back to since forever. In the dominant model, the deprotonated hydroxyl groups are complexed with Mg2+, at least two of ...
2
votes
1answer
50 views
What do ribbon diagrams mean?
What is the higher order meaning of ribbon diagrams like this one? I know the first order meaning is a graphical representation of α-helices and β-sheets, but what else does it mean? Is the protein's ...
0
votes
0answers
26 views
Ways to predict the preservation of functional domains in fusion proteins
My lab is synthetically creating fusion proteins consisting of an enzyme attached to a zinc finger through a linker. We can attach the zinc finger to the enzyme at either its N-terminus or its C-...
1
vote
0answers
33 views
What is the structure of PduK in the Pdu BMC?
My lab is creating 1,2-propanediol utilization bacterial microcompartments (Pdu BMCs) with an operon containing genes for PduA, PduB, PduJ, PduK, PduN, PduU, and PduT. According to Mayer et al., all ...
4
votes
0answers
28 views
Are all organelle lumens a reducing environment like the cytosol, or nonreducing like the extracellular space and the ER lumen?
I am interested to know if cysteine can form disulphide bridges in proteins within organelles. Typically cysteine will not form disulphide bonds in the reducing environment of the cytosol, but will in ...
2
votes
1answer
67 views
What is the point of calculating extinction coefficients of a protein without Cys residues?
ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value ...
4
votes
1answer
79 views
What is meant by “unique ligand” on the RCSB Protein Data Bank website?
I went to the https://www.rcsb.org/ site, and searched for some proteins. For each entry, “unique ligands” are listed.
I understand a ligand is a molecule or ion that binds to a metal atom. I don’t ...
1
vote
0answers
32 views
Differentiating molecules based on peptide sequence? How to annotate?
I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
0
votes
1answer
63 views
SARS-CoV - relative size of the spike protein
I was given the task of determining the percentage of the S-protein of the SARS-CoV relative to the total of its proteins from the attached image. However, I have been given no explanation of the ...
-2
votes
1answer
62 views
What is the thickness of the membrane if only alpha helixes are embedded of a transmembrane protien?
Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å
Please read:
The reason I didn't submit my ...
3
votes
1answer
72 views
Interaction of charged triphosphates with the ATP binding region in proteins
DNA-histone interactions involve positively charged amino acid side chains groups neutralizing the negatively charged phosphate of the sugar-phosphate backbone. Is the same true for ATP binding sites ...
3
votes
1answer
50 views
Using BLAST for molecular replacement in structural biology
This is my first time trying to do molecular replacement to solve a protein structure. I am using the NCBI blastp program to find suitable search models. When choosing a search model, I understand ...
-1
votes
2answers
43 views
How can predicting protein folding speed up drug discovery?
I'm asking this as a layperson without much knowledge in biology, so please correct me if my understanding is wrong.
Recently DeepMind's AlphaFold managed to predict protein structure from acid amino ...
1
vote
0answers
45 views
Why did the protein structure prediction accuracy in terms of GDT-TS decrease from 2008 (CASP 8) to 2014 (CASP 11)?
I read on https://doi.org/10.1038/d41586-020-03348-4:
Why did the protein structure prediction accuracy in terms of GDT-TS (Global Distance Test — Total Score) decrease from 2008 (CASP 8) to 2014 (...
0
votes
1answer
40 views
Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?
I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is ...
0
votes
0answers
49 views
Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software
I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have ...
0
votes
2answers
58 views
Why does sequencing virus proteins take time?
According to the below paper, the coronavirus spike protein sequence was available to scientists by end of february 2020 - the begin of march 2020 timeline. I had this question that why does ...
4
votes
2answers
311 views
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 ...
2
votes
1answer
15 views
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 ...
0
votes
1answer
233 views
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 ...
1
vote
1answer
27 views
Why is protein cyclisation desirable?
There are a number of methods to "cyclize" an existing peptide:
Disulphide bond as described in Disulfide Bond Mimetics: Strategies and Challenges by Gori et al.
"Linchpin" based (...
2
votes
1answer
57 views
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 ...
1
vote
2answers
174 views
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 ...
1
vote
0answers
33 views
Any kind of online "molecular modeling playground"?
I'm wondering if anyone has ever made a tool to try out new molecular modeling/simulation algorithms, where the tool itself handles the "boring" tasks of loading PDB files, building chains ...
0
votes
0answers
23 views
How to build SEG in your personal environment?
I'm trying to implement SEG (Wootton & Federhen,1993) in my MATLAB and Python environment. From this oriinal article I cannot figure out what I need to build my script. Are there any related ...
8
votes
3answers
370 views
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 ...
2
votes
2answers
94 views
How do you biologists draw a protein when you write a paper?
The following is one example of protein structure diagram that I want to put in my research paper. I took this from
Koniev, O. & Wagner, A. “Developments and recent advancements in the field of ...
0
votes
0answers
39 views
Why does insertion of transmembrane domains occur in the rough ER?
To elaborate on that question, why in the secretory pathway does the insertion of transmembrane domains into the membrane occur in the rough ER as the protein is translated and threaded across the ER ...
1
vote
0answers
31 views
What are good techniques for determining direct maps of proteins?
I am looking for which techniques to explore to determine electron density maps (or Fourier maps) for a protein (possibly using an assumed model).
In particular, I want to avoid techniques that ...
1
vote
1answer
116 views
Can the knowledge about torsion angles alone be sufficient for specifying secondary structures of protein?
I have read that Ramachandran plots are used to identify secondary structures of proteins. Also, alpha helices and beta strands cluster around specific regions of the plot which gives us the ...
0
votes
1answer
78 views
Glucose 6-phosphate dehydrogenase: reaction mechanism
I have searched the internet for the reaction mechanism of G6PD but couldn't find it, so I am asking whether anyone here knows its mechanism and whether they could recommend some sources that give ...
1
vote
1answer
58 views
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 ...
2
votes
1answer
58 views
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 ...
3
votes
0answers
41 views
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, ...
2
votes
2answers
156 views
Can 1.5 gigabytes encoded in the human genome really account for the complexity of a human being?
I read the human genome is 1.5 gigabytes in size. Thats actually not a lot; Photoshop probably takes more space. Mac OS takes 10+ gigabytes of space. Also, the genome is 1.5 gigabytes when counting ...
1
vote
0answers
21 views
What is the native structure of amyloid-beta protein under physiological conditions?
The amyloid-beta protein forms cross-beta structured fibrils. But under normal physiological conditions what is their predominant secondary structure. Is it alpha-helix, random coil or beta-sheet?
1
vote
2answers
110 views
Software to model and analyse protein–ligand interactions
I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding ...
0
votes
1answer
137 views
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 ...
3
votes
1answer
67 views
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 ...
2
votes
3answers
336 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 ...
1
vote
1answer
80 views
Protein structure prediction using PSSM? Or not?
I have been studying protein structure prediction algorithms. A lot of recent work uses something called the PSSM, the position-specific scoring matrix.
I think that what a PSSM does is to build a 2-...
0
votes
0answers
104 views
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 ...
3
votes
1answer
74 views
Emergence of novel protein interactions by mutation of amino acids
Are there any examples of proteins that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other protein ...
1
vote
0answers
21 views
Where can I find and download HMMTOP training set?
I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the ...
5
votes
1answer
185 views
Backbone hydrogen bonds between adjacent amino acids in a protein?
Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO?
Are there any examples of such situations in proteins and how common are they?
If ...