19
votes
Accepted
How hard it is to determine a 3d structure of a protein?
Experimental protein structure determination is hard: the most common method is X-ray crystallography, which can be done in a few months if you are lucky and can take years if you're not. The problem ...
- 4,371
14
votes
How hard it is to determine a 3d structure of a protein?
I'll address NMR for structure determination. It is the less common method, only ~10% of protein structures are determined this way, though it has e.g. advantages for nucleic acids and more than a ...
13
votes
In which direction does ATP synthase rotate?
Short answer
The direction of rotation depends on the viewing point of the observer and the reaction catalyzed by the ATP synthase. When synthesizing ATP, and viewed 'from the bottom' (observer faces ...
- 52.2k
12
votes
Accepted
Does the recent concern over several papers about Aβ*56 call into question the association of Alzheimers Disease with any amyloyd beta oligomer forms?
Does the recent concern over several papers about Aβ*56 call into question the association of Alzheimers Disease with any amyloyd beta oligomer forms?
From my understanding, no. alzforum.org has ...
- 1,855
9
votes
Is prion a term used to describe the normal form of the protein as well as the disease causing form?
If we are considering prions in general, I disagree with the answer supplied by Gerardo Furtado.
Here is a definition taken from an article by Susan Lindquist:
[Prions are]...self-perpetuating ...
- 22.7k
9
votes
Accepted
What are the different types of helices in protein secondary structures and how do they differ?
This DSSP page makes it clear that:
Helix-3 = 3-10 helix
Helix-5 = π-helix
The α-helix is described in every biochemistry text book and widely on the web. It has 3.6 residues per helical turn and ...
- 23.8k
9
votes
Accepted
What is meant by “unique ligand” on the RCSB Protein Data Bank website?
Your understanding is incorrect. A ligand at its most basic is a molecule that binds to another molecule. There is no requirement for metal atoms whatsoever. In the context of RCSB (home of the ...
- 23.8k
8
votes
Accepted
Should there be separate Ramachandran plots for an amino acid in different contexts?
The phi and psi dihedrals describe the dihedral on both sides of the c-alpha of a single amino acid, and do not involve any angles of the neighboring amino acid.
The Ramachandran plot is something ...
- 1,463
8
votes
Accepted
Denaturation of protein
If you think about the boiling of water, I'm sure you can understand that heat breaks hydrogen bonds. Next consider that the hydrophobic effect is driven entropically and so, by the equation $\Delta G=...
- 17.6k
8
votes
Accepted
Backbone hydrogen bonds between adjacent amino acids in a protein?
The situation you ask about was originally part of the 27 ribbon and 2.27 helix structures considered as possibilities by protein chemists (Linus Pauling?) in the 50s or 60s. The diagram below, ...
- 23.8k
8
votes
Why isn't the Ramachandran plot symmetric?
but only the Ramachandran plot for glycine shows this symmetry
With the exception of glycine, all the common amino acids exhibit chirality at the carbon atom adjacent to the carboxyl group.
Except ...
- 8,216
8
votes
Accepted
Is there are theoretical limit to the number of proteins possible and their respective structure?
You can certainly estimate a theoretical limit, given some assumptions.
Let's say you do not care about any post-transcriptional modifications, you are interested only in the primary sequence. There ...
- 1,554
7
votes
Accepted
Program (on Mac) to show 3D protein structures?
Jmol: how to install
Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC).
Download Jmol ...
- 23.8k
7
votes
Accepted
Difference between prions and amyloid proteins?
Amyloids are protease resistant insoluble fibrils formed because of (mis)folding and aggregation of soluble proteins (Rambaran and Serpell, 2008, Sabate et al., 2015). The first definition of prion ...
- 35.2k
7
votes
Software to model and analyse protein–ligand interactions
I don't know precisely what you mean by "analyze", which could be anything from simply "view" or "measure distances", to evaluating an energy function on a crystal structure or molecular dynamics ...
- 393
7
votes
Why isn't the Ramachandran plot symmetric?
It's awkward answering your own question, but I think I have now realized where my misconception arose from.
If we look at the 3 dimensional structure of a protein
and consider the third alpha carbon ...
- 159
7
votes
Is there a way to refine a low resolution Cryo-EM structure using high resolution partial crystal structures?
You should use the original electron density map, not the atomic coordinates associated with it.
Other than that, what you are describing is fairly routine. Briefly, the high resolution structure is ...
- 3,536
6
votes
Accepted
Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?
Yes, there are certain amino acid sequences that tend to form alpha-helices, and others that prefer to form beta-sheets. There is no perfect correspondence between sequence and structure, but there is ...
- 5,625
6
votes
Accepted
What is an isolated beta bridge?
In Kabash and Sander's paper related to DSSP (Biopolymers 1983 vol. 22 (12) pp. 2577-637) the following appears in the abstract:
We have developed a set of simple and physically motivated criteria ...
- 23.8k
6
votes
Accepted
Resolution of X-ray crystallography
The structural model of a protein is obtained using both experimental data and prior knowledge about geometry of macromolecules. As a structural model is refined, interatomic distances are also ...
- 449
6
votes
What is peptide mapping?
Shimadzu explains peptide mapping as follows:
Peptide mapping involves selectively cleaving the individual target [proteins] using an appropriate enzyme or chemical and analyzing the peptide ...
- 52.2k
6
votes
Accepted
Do non-functional (‘junk’) protein sequences exist?
This question is unanswerable as, if a protein exists as a physical entity in a cell it is possible to demonstrate it has a functional or structural role, but it is logically impossible to demonstrate ...
- 23.8k
6
votes
Accepted
When does protein folding begin?
When does protein folding begin?
With reference to time you have asked, it can be after the translation has occurred (called Translational protein folding) or while translation is still occuring (...
- 360
6
votes
Accepted
Why does the structure for cellular retinol binding protein show interactions with cadmium ions?
As far as I am aware, there is no known requirement for Cd in mammalian systems, but it is extremely toxic (Waalkes & Goering).
It would seem that cadmium is required to get crystals of RBP, and ...
- 4,668
5
votes
Accepted
Generate full dimer from monomer with C2 symmetry?
This article will probably be informative for you:
Looking at Structures: Introduction to Biological Assemblies and the PDB Archive
The PDB file contains the asymmetric unit found in a particular ...
- 17.6k
5
votes
Accepted
Proteins in water vs proteins in crystal
Protein crystals are not like crystals of more commonly found substances like salt [NaCl] or diamond [carbon only.] These materials do not include other atoms in their crystal structures. For ...
- 111
5
votes
Accepted
What is the significance of cysteine in a protein sequence?
What can I infer if I get a high percentage of C from a protein
sequence?
A highly stable structure that is likely found in the extra-cellular space.
Cysteine can form a disulphide bond with ...
- 11.3k
5
votes
Should there be separate Ramachandran plots for an amino acid in different contexts?
Some further observations about Ramachandran plots in response to the question:
They were originally calculated. This was done by considering the minimum contact distances shown in the diagram (which ...
- 23.8k
5
votes
Accepted
Are proteins a different shape in space?
Proteins are not made to be one way up or the other as they flow around and surround cells, so sea-level to space gravity gradient will not be the major cause of change to proteins at different ...
- 9,592
Only top scored, non community-wiki answers of a minimum length are eligible