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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Export AlphaFold Server file and visualize on PyMol
I am currently working with AlphaFold Server, which is Google DeepMind's public access release of AlphaFold3, a model for biomolecule structure prediction.
I am using it in order to predict protein-...
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How do you determine the structure of a molecular recognition feature (MoRF) after it binds to itself?
I have a protein that has a roughly 10 residue chain that registers at a MoRF in MoRFPred and MoRFchibi. I have the PDB files to correlate the known structure of the protein with the site of the MoRF; ...
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How is the "global pLDDT" score in the Protein Data Bank calculated?
Consider this list of entries for the Tobacco Mosaic Virus (TMV). I selected to sort by 'Global pLDDT' from best to worst. It is my understanding that pLDDT is usually calculated per residue for a ...
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Do right-handed helices bind to right-handed helices, and vice versa?
I know that B-conformation DNA is a right-handed helix, and most proteins that form helices form right-handed, not left-handed, helices (1). Furthermore, "Many transcription factors have an alpha-...
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Overlapping atomic radii in data of experimentally observed protein assemblies
I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M
When taking the atom centers of a monomer and ...
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If a protein has multiple globular domains with flexible peptide linkers in between, how do they fold?
Do they fold independently of each other or synergistically? If we express these globular domains separately, would their structures remain the same?
I came up with an easy way to test it. Many RNA ...
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How is opsin of rhodopsin is different from that of iodopsin? [closed]
Rhodopsin contain retinal, an aldehyde of vitamin A and opsin protein and iodopsin also contains retinal along three different types of opsins namely erythropsin, chloropsin and cyanopsin. But kind of ...
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Examples of Differential equations in Biology
I am a mathematician currently teaching some math classes at a university. Next semester, I'll have bachelor's degree biochemistry students. I want to know where certain math tools might be needed in ...
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RMSD / Tm metric for comparing local molecular structure similarity?
I would like to compare two molecular (protein) structures, but rather than comparing the total, global structures against themselves to yield an RMSD score (which would be straightforward with a ...
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Validating Generative Models for 3D Conformations of Inactive Dopamine Receptors in Protein Design
Considering a dataset comprising 3D conformations of Dopamine receptors in an inactive state, we aim to train a generative model capable of capturing the distribution of these receptors and generating ...
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Clustering collection of PDB files based on 3 dimensional structural similarity in python
I have generated a set of 3-dimensional structures of the peptide AGAGAG with different structures. Total number of PDB files are 300. I need to cluster the peptide structures based on their ...
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MSA cluster and MSA depth
I was reading the AlphaFold paper and had difficulty with a couple of terms introduced in the main text of the paper. I asked ChatGPT what these were but I'm not sure that it's accurate.
I had a hard ...
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Quantifying Hydrophobicity from amino acid sequence
fourth-year undergrad here so any help is super appreciated! Also this is not something I am working on for a grade, so pls don't think I am just looking for someone to do my homework lol!
In a gist, ...
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Question on protonation/deprotonation of amino acid side chains
I understand that actual pKa of amino acid side chains is greatly influenced by the surrounding environment. I am trying to deeply understand the equilibrium between protonated and deprotonated form ...
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If we were to discover an alien ecosystem that has a D-configuration of proteins, how would it react to our L-sided biology?
I'm concepting a hard-sci-fi story where a scientist discovers microorganisms in our solar system with disastrous results. I was thinking about how any cross-contamination with an alien ecosystem ...
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The meaning of atoms sign in protein structure
There are some atoms sign of protein structure in paper, like Nε2， Cε. I know this sign is for information about atoms position, but I don't know the exact meaning. The below is original words in ...
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Can one use DSSP (secondary structure assignment) for short peptides of size 6, 10 and 18?
I have large number of PDB files of peptides of size 6, 10 and 18. I wanted to cluster the peptide structure based on the secondary structure. I used DSSP in mdtraj module in python to assign DSSP ...
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Allowed Deviations in fixed bond length and bond angles in peptides from the typical values
I am using frag builder python module to generate peptide structures to compute the interaction energy for ensemble of peptides of a given sequence for a fixed bond lengths and bong angles. However, ...
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Antibody structural determinants of epitope size
I am curious whether there are structural correlates in antibodies that relate not to epitope sequence but to epitope size. Specifically, I imagine that the antibody-epitope interface size is ...
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Is there a way to refine a low resolution Cryo-EM structure using high resolution partial crystal structures?
I'm working on running simulations of human topoisomerase IIa. These are best done by starting with high resolution structures to ensure the system is as accurate as possible. However, no crystals ...
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What is the oligomeric state of Leptospira LipL32 protein?
Does anyone know the oligomeric state of the mature and functional lipoprotein lipL32 in Leptospira?
It's an outer membrane-bound protein. In its mature state, the signal peptide (residues 1-20) is ...
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Is it possible to crystallize proteins so that the crystal has a normal concentration of potassium chloride?
I've been learning about protein crystallography, and how crystals are made. A lot of the crystallization processes involve gradually changing variables (protein concentration, pH, salt concentration,...
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Protein crystal X-ray diffraction at room temperature?
It seems essentially all protein X-ray diffraction structures are obtained with flash-cooled protein crystals (in a stream of very cold gas). I’m curious if the diffraction pattern would be ...
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Why are there so many carbonic anhydrase structures in the Protein Data Bank?
I've been looking through PDB — the Protein Data Bank — and I noticed that the protein with the most structures is human carbonic anhydrase II (UniProt: P00918), with over a thousand X-ray 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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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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