Questions tagged [protein-structure]

The 3-dimensional organisation of amino acids in a protein, specifically including the secondary, tertiary and quaternary structures.

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Is there are theoretical limit to the number of proteins possible and their respective structure?

I saw an article saying that DeepMinds AI has catatogued every protein known to science. I guess "known to science" and what is the theoretical limit is not exactly the same thing but the ...
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Does the recent concern over several papers about Aβ*56 call into question the association of Alzheimers Disease with any amyloyd beta oligomer forms?

The news item by Charles Piller just published in Science BLOTS ON A FIELD? A neuroscience image sleuth finds signs of fabrication in scores of Alzheimer’s articles, threatening a reigning theory of ...
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Aligning two PDB structures with different numbers of atoms

What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both ...
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T-Cell Receptor Receptor-Associated Immune Receptor Activation Motifs (ITAMs) Inconsistency

In reading the information associated with the cytoplasmic machinery of the T-Cell Receptor (TCR), the one tyrosine motif that is consistently mentioned is the receptor-associated immune receptor ...
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Why isn't the Ramachandran plot symmetric?

Since only relative position of groups along a bond is considered while calculating torsional strain and considering "+" and "-" means clockwise and anti clock wise rotation, ...
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What is meant by ‘local structure’ of proteins?

The EBI/EMBL training course includes the following definition of Secondary structure of proteins: Secondary structure refers to the regular, local structure of the protein backbone, stabilized by ...
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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 ...
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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 ...
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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 '...
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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 ...
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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/...
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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 ...
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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 ...
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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-...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 (...
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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 ...
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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 ...
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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 ...
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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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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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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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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 (...
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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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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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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 ...
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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 ...
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3 answers
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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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2 answers
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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2 votes
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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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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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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 ...
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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?
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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 ...
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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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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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