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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 ...
Nicolai's user avatar
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15 votes
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Examples of Differential equations in Biology

For biochemistry students the obvious link to differential equations is the Michaelis–Menten equation which is a simple model of the kinetics of reactions involving enzymes. Your students will be ...
Charles E. Grant's user avatar
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 ...
Mad Scientist's user avatar
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 ...
AliceD's user avatar
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13 votes

Examples of Differential equations in Biology

Update please follow Charles E. Grant's advice and do Michaelis-Menten! Hodgkin-Huxley as suggested by commenter ctwardy is a great idea too. Original answer I would strongly recommend the book ...
Maximilian Press's user avatar
12 votes
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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?

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 ...
Franck Dernoncourt's user avatar
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 ...
Alan Boyd's user avatar
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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 ...
David's user avatar
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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 ...
David's user avatar
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9 votes
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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 ...
Domen's user avatar
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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 ...
VonBeche's user avatar
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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=...
canadianer's user avatar
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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, ...
David's user avatar
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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 ...
acvill's user avatar
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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 ...
David's user avatar
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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 ...
WYSIWYG's user avatar
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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 ...
biohacker's user avatar
  • 409
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 ...
veke's user avatar
  • 259
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 ...
timeskull's user avatar
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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 ...
David's user avatar
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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 ...
Roland's user avatar
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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 ...
David's user avatar
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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 (...
Science123's user avatar
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 ...
user338907's user avatar
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6 votes

Examples of Differential equations in Biology

Are Twelve ODEs for mitochondrial membrane potential (ΔΨm), and matrix concentrations of Ca2+, NADH, ADP, and TCA cycle intermediates, used to model the response of mitochondria to changes in ...
user21820's user avatar
  • 386
6 votes
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If a protein has multiple globular domains with flexible peptide linkers in between, how do they fold?

A broad interpretation of the question The question refers to the “folding” of proteins. This term — and the associated biological problem — is often used in the rather specific sense of the ...
David's user avatar
  • 25.7k
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 ...
James's user avatar
  • 11.3k
5 votes
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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 ...
Edward Kowal's user avatar
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 ...
David's user avatar
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