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11

Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring ...


6

in silico modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally. From the Folding@Home website: Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation ...


6

These are are completely different concepts, which sometimes may be connected. A motif in biology is a mathematical model, typically of a sequence, which is predictive of which sequences to some defined group. For example, a DNA sequence motif can characterize the binding site of a transcription factor, i.e. which sequences tend to be bound by this factor. ...


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Hsp70 and Hsp90 are not single proteins, but entire protein families. And those two protein families are not the only ones of their kind. There are different groups of heat shock proteins, Hsp70 and Hsp90 are molecular chaperones that assist in protein folding. There are five major families of molecular chaperones: Hsp100, Hsp90, Hsp70, Hsp60 and Hsps. ...


4

Often cells have multiple types of the same protein — this redundancy can have different effects for different requirements such as having proteins function under different physiological conditions, or providing specificity to a certain class of ligand proteins or so on. But here, it seems like the two have some synergistic interaction, a tag team if you ...


4

The main problem is that Mad Cow disease is not caused by a "normal" pathogen but by a prion, a protein. Traditionally, disease causing agents can be classified into viruses, bacteria, fungi, and parasites. Bacteria, fungi and parasites are all living organisms, alive in the traditional sense. It is, therefore, possible to design drugs that kill them. ...


4

If the process of evolution is driven by completely random process... It's not. The evolution of "better" protein (and other) molecules happens because of selection, a very non-random process. The repeated selection of better molecules, and then of the variants of the better molecules, repeated many times, will lead to "good" molecules (in the sense ...


4

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 ...


4

Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional. Alanine scanning is a technique that methodically replaces amino acids in a ...


4

Are multi-chain proteins synthesized as one biological unit? Sometimes yes but mostly not. Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this ...


3

1) Is the attachment of zinc regarded as a type of post-translational modification? It is not really considered a post-translational modification because the zinc atom is not covalently bound to the protein. Binding to zinc is adsorption. 2) When carbonic anhydrase is denatured, is the zinc ion released in the medium? Yes, but it depends on ...


3

3D structure. Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what ...


3

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 ...


3

I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper. And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though. At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal ...


3

I am also about to undertake some FRET studies (this week in fact). FRET linkers are a thing of tinkering, unfortunately. Förster resonance energy transfer, or FRET, is a phenomena that decays with $ 1/{r^6} $, the radius between the donor and acceptor. When constructing FRET reporters, there are a few things to keep in mind: Length of linker. The length ...


3

One of the quickest ways to get oriented on what is going in the world of protein folding and modeling is to look at the proceedings of the Critical Assessment of Structure Prediction (CASP). CASP is basically a contest, held every 2 years where anyone can use their algorithm to predict the 3D structure of a protein whose structure is known, but not ...


2

Since we only have one planet that we know of with life, it's a bit difficult to make good estimates on the probability of various events in the history of life. To make a good estimate, you'd want to have thousands of planets very similar to earth to compare. Since we don't have access to that kind of data, one proxy which you can look at is how long did ...


2

Exactly how genetic material changes from one generation to the next is a very complex subject. But essentially you are right. The change in genes from one generation to the next is not only mutations though. It is also mixing of the genes carried by the male and the genes carried by the female. The selection process is also very complex, and sexual ...


2

The principal difference is that domains are independently stable, while motifs are not. Here is a bit on motifs: http://www.sinauer.com/pdf/nsp-protein-1-16.pdf A motif can be part of a domain. From there: The second, equally common, use of the term motif refers to a set of contiguous secondary structure elements that either have a particular ...


2

All the residues in a polypeptide chain tends to configure into their lowest potential energy state. except the peptide bond all the other bonds are free to rotate, alpha helix makes optimal use of internal H bonds. The overall structure is stabilized by H bond between the hydrogen atom attached to the electronegative nitrogen atom of peptide linkage and the ...


2

I'm going to assume that you mean "are there any rules for which amino acids can follow which amino acids in a protein?" The answer is no. In terms of a protein's chemistry, there is no restriction on the amino acid sequence. However, not all amino acid sequences will fold into a definite 3D structure, and not all amino acid sequences will be soluble in ...


2

Short Answer What mathematical work is currently being done in this area? A... lot? Longer Answer The "n-dimensional slope" thing that you're talking about shows up in the modern theory of protein dynamics as the "landscapes" concept. There's no truly standardized form for the theory, so it goes by many names. Try googling folding funnel, energy ...


1

TMHMM is a very good standard on predicting the TMHs in the first place, so it stands to reason that predicting homologues using this approach is completely viable.


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Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary ...


1

I will try answer your question directly. How do we know if we fold it right? A. If you're interested in only the end product pf folding -- the 3D structure, then this is the subset of the folding problem called the structure prediction (from sequence alone). a. We can verify the structure experimentally by determining the 3D structures by NMR or ...


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A certain fold of a peptide string can be validated or ruled out if other experimental data is available. Some other techniques to infer protein structure are X-ray crystallography (requires pure protein that will crystallize) and single particle analysis.


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I hope that I got what are you asking. You give the example of words, it's not good one. Look on the protein like a machine or maybe cupboard. You bought one in Ikea and now you need to follow the instruction to bring together all the elements. If you just paste together all the parts you will not get a working cupboard. What rules the parts of cupboard ...


1

I suppose you are not asking how does DNA code for mRNA which has codons (sets of 3 nucleic acids) when read in the correct reading frame (where 3 base pairs each are read beggining from the start codon) a ribosome then translates this into protein... theres a lot more details then what I said... that is called translation: ...



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