The study of the molecular structure of biological macromolecules and how that structure relates to their function.

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Determine if two molecule structures are the same molecule (perhaps in different conformations)?

I have two .pdb files describing two (small ligand) molecular structures. I need to determine if these two pdbs describe the same molecule, perhaps in different spatial conformations. Is there a ...
2
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0answers
20 views

Can a stationary eye with a moving pupil exist? [closed]

I am making a sci-fi web-comic set on an alien world and I thought up an idea for an eye that works much like an eye from a mammal, but instead of moving the whole eye, only the pupil moves. This idea ...
0
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0answers
11 views

Web repository to predict secondary structure of protein the the form of H C and E

Is there any website which would take in as input multiple amino acid sequences and output the secondary structure in the form of H(helix) C(coil) and E(strand)? I found this website but it cannot ...
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0answers
16 views

Normalise protein database domain-wise

Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several ...
4
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2answers
92 views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
0
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0answers
11 views

Biomolecule , DNA-RNA difference [duplicate]

Why is that a RNA has uracil in place of thymine? RNA could have thymine bases but it has uracil ? What is the reason for the presence of uracil there ?
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0answers
34 views

Can I explain the kinetics of a ligand looking at the ligand-protein co-structure?

Can I explain the kinetics of a ligand binding to a target protein (association and dissociation rates) by looking at the protein-ligand co-structure? Editing my question after a few comments: I ...
1
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0answers
17 views

Differences in structural target for LPS detection by LAL and MD-2/TLR4

I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte ...
2
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0answers
14 views

What is internal symmetry in membrane proteins?

I have come across the term "internal symmetry" in the context of membrane proteins, but have never found a satisfactory definition. I'm struggling to figure out exactly what this term means... What ...
7
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85 views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
4
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1answer
75 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page ...
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49 views

Is the number of stamens always 9 for geranium?

We are studing in class the reproduction of plants. We start the lesson by observing some components of flowers, it was the Géranium. First of all we start counting the number of sepals , petals and ...
0
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1answer
40 views

Using Jpred to predict secondary structure

I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i ...
3
votes
1answer
69 views

Simplified molecular-input line-entry system

This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer. What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is ...
6
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0answers
70 views

DNA-DNA cross-linking with formaldehyde?

The 3C (chromosome conformation capture) technology for studying chromatin 3D organization starts by a cross-linking step using formaldehyde to find segments of DNA interacting. In my understanding ...
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0answers
240 views

How can the directionality of a protein structure be defined?

For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on ...
6
votes
1answer
240 views

What allows Valonia ventricosa cells to get so big?

Valonia ventricosa are single celled algae that range between one and few centimeters. In rare cases they can reach sizes exceeding 5cm. They range from grass green, to dark green, and some are even a ...
0
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1answer
1k views

Why do the major and minor groove exist in DNA?

So I know that the major/minor groove arise from the offset pairing of the two strands in the helix. All my textbook tells me is that "pitch causes the off-set pairing of DNA and this gives rise to ...
0
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1answer
40 views

About molecules and their shape

When a molecule is being used in some biochemical process it has a certain 3-d structure. Is this maintained throughout it's usage or can one specific molecule change it's 3-d shape while it is being ...
3
votes
1answer
80 views

How to recognize a conserved motifs of the protein

I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids ...
4
votes
1answer
119 views

Topology of closed circular DNA

Why are covalently closed circular plasmid DNAs naturally found in an underwound state ? Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it ...
2
votes
1answer
123 views

how do they identify different protein chains?

Can someone please explain how different protein chains occur exactly? I'm not talking about the side chain, but the protein chain which is typically labelled as A,B,C etc in the PDB. I'm curious as ...
6
votes
1answer
51 views

Are original x-ray diffraction data available

Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these ...
4
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0answers
271 views

Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA [closed]

We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The ...
4
votes
1answer
233 views

Stability of helical strands of DNA?

The DNA molecules contain phosphate groups involved in $3'\rightarrow 5'$phosphodiester linkages. These groups, in the bonded state with deoxyribose, contain 1 negative charges ($\ce{3'-PO4^{-}-5'}$). ...
4
votes
1answer
99 views

Which of Perutz et al's protein structures other than 3₁₀ helix were correct?

In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, ...
4
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1answer
4k views

Isotropy of sarcomere bands in skeletal muscle cells

As seen under a polarization microscope, the A-Band in skeletal muscle fibres is so named because it is anisotropic in its refractive index which is a characteristic of orderly crystalline structure. ...
2
votes
1answer
118 views

Are there known 3- or 4-nucleotide RNA linkers with no RE sites?

Question is rather self-explanatory. I'm looking for a non-cleavable RNA sequence to act as an RNA linker. I mention 3- or 4-nucleotides only, but making such a sequence with 2 nucleotides is rather ...
4
votes
3answers
571 views

What are the benefits of elucidating the crystal structure of a protein?

I have spent months as a student working on trying to form a tricky protein crystal. But I have never actual had explained to me why the structure will be useful. Once elucidated, what can we ...
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vote
1answer
50 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
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0answers
37 views

Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
1
vote
1answer
67 views

Is there a way to see what representations are currently displayed in PyMOL?

I am using PyMol to visualize .pdb protein structures. I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
4
votes
1answer
783 views

How do I view the simulated protein structure along with ligand in VMD?

I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
2
votes
1answer
68 views

PTMs of proteins via mass spec?

I understand that mass spec is widely used to study PTMs like glycosylation of proteins, but how can mass spec determine correct PTM structure of say glycosylation if two glycan structures have the ...
2
votes
3answers
118 views

What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
14
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1answer
462 views

Fibonacci sequence in nature, truth or just wishful thinking?

I'm reading a bit on the Fibonacci sequence in nature, be it the golden ratio or the golden spiral forming over and over again in biological structures, and then I came across this online article by ...
5
votes
1answer
144 views

Structures of cyclodextrin complexed with small ligands

For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, mol2, etc) complexed with small molecule ligands, such as cholesterol and even smaller. Right now I could ...
3
votes
3answers
515 views

What is a good list of unsolved protein structures?

I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein. Things that ...
4
votes
1answer
72 views

Parse PDB using DSR-PDB Library

I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose. I've encountered a problem. This library interprets CD1 atom of ILE ...
8
votes
0answers
546 views

Rosetta ab initio prediction and protein-protein interaction fitness help [closed]

I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to ...
3
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0answers
136 views

RMSD during conformational transition in proteins

When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved ...
4
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1answer
118 views

Is there an advantage to having cellulite

There are many ads nowadays advertising cellulite removal, and it causes me to wonder if there is an advantage to having cellulite or if it is just a result of too much fat unevenly spread? Is it ...
3
votes
2answers
425 views

JMol “calculate HBONDS”: which atom is the donor/acceptor?

JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds. Here's one line from an example ...
10
votes
1answer
160 views

Protein data bank syntax: Can two protein secondary structures “overlap”?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
4
votes
1answer
95 views

How would one describe the R-factor in crystallography?

Yes, there is the wikipedia definition, but how would one explain this concept to a non structural biologist?
3
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2answers
338 views

Two subunits connected by only one disulfide bridge: quaternary structure?

I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides ...
5
votes
1answer
228 views

Are quaternary protein monomers unique to a particular protein complex?

I know that quaternary protein structures are formed exclusively via non-covalent bonds. My biochemistry professor discussed a viral capsid that is essentially one quaternary structure with 240 ...
8
votes
2answers
229 views

Solution based measurement of Solvent-Accessible Surface Area of macromolecules

The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA ...
12
votes
1answer
8k views

What is the significance and method behind Ramachandran plots?

My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and ...
5
votes
1answer
118 views

How do I prepare a PDB for submission to the Protein Data Bank?

I have a couple structures that are nearly ready to be deposited in the PDB. Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked ...