19 votes
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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 ...
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  • 4,296
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 ...
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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 ...
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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 ...
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9 votes
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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 ...
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9 votes
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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 ...
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8 votes
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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 ...
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  • 1,453
8 votes
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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=...
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8 votes
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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, ...
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7 votes
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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 ...
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7 votes
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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 ...
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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 ...
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  • 393
7 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 ...
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  • 7,214
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 ...
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  • 149
6 votes
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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 ...
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  • 374
6 votes

Are There Rules for How Proteins Are Formed?

It sounds like your question is "what are the rules to protein folding?" That's not the only way to read your question. Protein Folding is a unique problem - a 1D sequence maps to a 3D object. ...
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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 ...
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6 votes
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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 ...
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6 votes
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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 ...
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  • 5,595
6 votes
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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 ...
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6 votes
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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 (...
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6 votes
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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 ...
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  • 4,638
5 votes
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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 ...
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5 votes
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NMR spectroscopy detection methods for proteins

In most cases when you perform NMR experiments on proteins you detect the signal on the protons. Even if you're looking at other nuclei, in the end you transfer the magnetization to a proton and ...
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5 votes
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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 ...
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  • 11.2k
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 ...
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  • 22.3k
5 votes
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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 ...
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5 votes
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What is C-terminal tryptic peptide?

Its quite simple if you look at the basics! Lets have a look at the sequence you give: AGWRGSDSHSR Write that in 3-letter terms1: Ala-Gly-Trp-Arg-Gly-Ser-Asp-Ser-His-Ser-Arg Pay attention to ...
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5 votes
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Protein structure prediction from amino acids sequence

what is the accuracy we can predict tertiary protein structure That depends on the protein. If the primary sequence closely matches the sequence of a protein for which the structure is already ...
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