19

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 with X-ray crystallography is that you need good protein crystals, and in most cases, proteins don't crystallize very well, so it takes a lot of time (and a lot ...


14

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 third of those was solved by NMR. Take any numbers here as very rough estimates, there are a lot of factors that influence the difficulty and cost. For NMR, the ...


11

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 the intermembrane space looking into the mitochondrial matrix) it rotates clockwise. Background ATP synthase is a membrane bound enzyme with two large subunits;...


9

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 and heritable protein conformations that cause multiple phenotypes, represent an unusual mechanism of information transfer that occurs via protein instead of ...


8

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 $\Delta G=\Delta H-T\Delta S$, its strength increases with temperature (to a point). See here and here for further explanation. Also, this paper for a more empirical ...


8

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, showing the ribbon, is from the classic text (long out of print) The Structure and Action of Proteins by Dickerson and Geis. This turns out to be very rare in ...


7

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 generated from a set of protein structures, an empirical data set. The top graph represents the dihedrals found for all non-glycine residues in a set of ...


7

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 from https://sourceforge.net/projects/jmol/files/latest/download?source=files The name of the file will be something like Jmol-14.29.16-binary.zip. Double-...


7

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 simulation, to prediction of binding sites de novo. The tools are different for each case, though some can do several things. For simply viewing, measuring ...


6

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 restrained. So, the C-N distance isn't really predicted. Alternatively, knowledge about this distance is used to construct reasonable model. In response to the ...


6

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 fragments obtained using HPLC [high-performance liquid chromatography] or another suitable method. [... I]dentification of the peptide fragments separated by LC [...] ...


6

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 was given by Prusiner (1982): Because the novel properties of the scrapie agent distinguish it from viruses, plasmids, and viroids, a new term "prion" is ...


6

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 its presence is an artifact of the crystallization process (ref): Pig holoRBP crystals were obtained at 277 K by the sitting-drop vapor- diffusion method, ...


5

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 for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative ...


5

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 detect that signal. This is simply the most sensitive method due to the high gyromagnetic ratio of 1H, and this is the method that is labeled "inverse" in your ...


5

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. Since proteins mediate nearly all biochemical transformations and therefore mediate life's processes, protein folding one of the great unsolved problems in ...


5

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 crystallographic study. The biological assembly is the quaternary structure known or predicted to be found in living systems. For many proteins (but not 2PJY), the ...


5

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 a statistical relation where presence of certain amino acids in particular sequences makes one conformation or the other more likely. For example, alanine, ...


5

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 another cysteine. Cysteine can be found as a lone cysteine, but is often paired with another cysteine in the tertiary structure to form these bonds. Disulphide ...


5

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 altitudes. Pressure is more of a factor on proteins, and it has been studies very much, both for protein shape and protein interaction with elements and other ...


5

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 it has no such role. The best one can say is that “it has no known function (role)”. That said, in the course of evolution following gene duplication and ...


5

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 the C-terminus. The last amino acid residue in the sequence is Arginine. Now, its well established that Trypsin cleaves a polypeptide after (i.e. towards the C-...


5

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 (called Co-Translational protein folding). Here is the link to an article for basic understanding of co-translational protein folding. There is a lot of debate on ...


4

Preamble In the comments @CMosychuk linked the most comprehensive text on ab initio I have seen this side of the year 2000 (Lee et al., 2009). It agrees that you've raised a good point. It is important to acknowledge that ab initio prediction methods solely based on the physicochemical principles of interaction are currently far behind, in terms of ...


4

Disclaimer: This is an interesting question if I have understood what you are trying to ask. But unfortunately the case is that there are so many different cases its impossible to cover them here. Other answers talk about folding and modification, but these are still heavily dependant on the "2d" DNA sequence and aren't useful if all one has is a final ...


4

Apparently the trans configuration is more stable, so more amino acids with a trans configuration can be found within a polypeptide chain. Does this pose any significant characteristic to a protein, and if so what is this characteristic? As you said, the trans- form is energetically more favourable. However, in proline the cis- form is energetically ...


4

Peptide bonds (also called amide bonds) are definitely covalent bonds. This is also mentioned in the first line of wikipedia entry: https://en.wikipedia.org/wiki/Peptide_bond


4

Protein found in a biological system with a unique three-dimensional structure and biological activity is called a native protein. When a protein in its native form, is subjected to physical change like change in temperature or chemical change like change in pH, the hydrogen bonds are disturbed. Due to this, globules unfold and helix get uncoiled ...


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