Questions tagged [structural-biology]
For questions related to the molecular structure of biological macromolecules (especially proteins and nucleic acids), how they acquire the structures they have, and how alterations in their structures affect their function.
72 questions
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How to understand the contour plot of NMR data of peptide reconsituited into mechanical oriented DMPC membrane?
I need help understanding the contour plot I mentioned. I have two questions:
How do the authors relate the topological restraints to the theoretical model? As I understand it, the tilt vs. pitch ...
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How does Ag+ interact with Cl-?
$\ce{Ag+}$ is an effective antimicrobial, but $\ce{AgCl}$ is not.
Would mixing $\ce{Ag+}$ with hydrochloric acid cause all of the silver ions to form $\ce{AgCl}$, or is there a saturation point ...
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Protein quaternary structure in ViewLite
I want to represent the octameric structure of a metalloprotein in the ViwerLite program. I loaded the PDB file related to the protein, but the progranul only displays a monomeric structure (a single ...
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Which position do retro aldol reactions occur in (comparing glucose and fructose)?
Regarding glycolysis, my text states:
What is the biochemical rationale for the isomerization of glucose 6-phosphate to fructose 6-phosphate and its subsequent phosphorylation to form fructose 1,6-...
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Where are the N and C-termini located in hemoglobin?
I am trying to locate the N and C terminus of hemoglobin and cannot tell if the C is at Val-1 and the N is Arg-141.
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Is it possible to have an anhydrous solvent for virology, specifically in vitro phage assembly?
Typical protocols for lambda phage in vitro assembly call for you to dump all your viral components and buffer solutions into water. Water is a great solvent, drives extraction of energy from atp, and ...
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Difference between Protoporphyrin and Porphyrin? [closed]
I understand that Porphyrin is defined as 4 pyrole rings linked by methenyl bridges. When this porphyrin ring is associated with a Ferrous ion (Fe 2+) we get the Heme molecule. However my book ...
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How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?
So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
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How to model CRISPR/Cas9 binding and cleavage using a generalized Kittel's zipper model?
I am thinking about how to model the binding of a CRISPR/Cas9+guide-RNA complex to a double-stranded DNA that cause its cleavage.
This post describes four steps at which a CRISPR/Cas9 system binds and ...
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Is Porphyrin Planar?
I have been looking at this diagram from quite some time, I know the 18 pi electron cycle that forms porphin(e) is definitely planar but what about the whole molecule?... The Nitrogen's act as a ...
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What could these letters "S" in red circles mean in a biochemical diagram?
What could be the meaning of the red circles with letters S in them in the diagram below? I searched in the text but could not find.
From "Role of TREK-1 in Health and Disease, Focus on the ...
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Does migraine medicine Topiramate work by supplanting Pyridoxal phosphate in enzymes?
I have seen it said that the precise mechanism of action of migraine medicine Topiramate is not known. But I certainly see a resemblance between that molecule and PLP (Pyridoxal phosphate, the ...
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How does the Benedicts Test work? [duplicate]
What exactly is the mechanism by which Benedict’s test works for reducing sugars? As I understand it the free hemiacetal groups on reducing sugars opens up and an aldehyde is formed, this is then ...
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Which textbook is this image on protein tertiary structure from?
I am trying to find the original textbook image that is the inspiration for many schematic figures showing tertiary interactions (hydrogen bonding, ionic interactions, hydrophobic interactions, ...
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Are crystallographic omit maps only used with molecular replacement?
(This is in the context of macromolecular X-ray crystallography.)
From Lamb et al. 2015:
Model bias is the result of how maps are calculated: because the
phase estimates [of the structure factor] for ...
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Is a beta pleated parallel sheet always formed from more than one peptide?
I can conceptually grasp the beta pleated anti-parallel sheet by imagining a curved length of string i.e. one polypeptide, starting with the N- terminus on the left and ending with the C-terminus at ...
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What exactly is peptone (tryptone?) and why does it not get precipitated?
According to Wikipedia Peptone (also called Tryptone) is a form of amino acid that has been treated by stomach acids. According to Google it also stays in solution when treated with acids or heat. Why ...
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Distance requirement for hydrogen bonding to occur
I am trying to understand the distance requirement for hydrogen bonding to occur (more specifically in the context of protein folding). There needs to be a donor and acceptor atom for bonding to occur....
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Preferred IUPAC name of Protoporphyrin IX
I was looking up protoporphyrin IX and was surprised to find that no two websites gave the same IUPAC name for the compound. Here are some examples:
3,3'-(7,12-Diethenyl-3,8,13,17-...
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What is the structure-activity relationship of cocaine?
Cocaine is a widely known drug for both recreational and pharmacological uses. What exactly is the relationship of its structure to its drug activity?
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Is hydroxychloroquine an anti-psychotic drug? [closed]
Is hydroxychloroquine an anti-psychotic drug or psychotic drug?
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Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]
I am completely new to using OpenBabel software.
I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them....
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How can subtilisin still function without its catalytic triad?
I read chapter 9 in the book Biochemistry (5th edition), by Berg, Tymoczko, and Stryer (provided in the NCBI site here). It describes the mechanism of action of the chymotrypsin enzyme. The catalysis ...
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Molecule with reversible exothermic conformational change?
I proposed some exotic biochemistry on the Worldbuilding stack.
https://worldbuilding.stackexchange.com/questions/166814/digestive-system-of-the-ultimate-omnivore/166829#166829
Your creature ...
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What Is the Difference Between Radiation and Radioactivity? [closed]
Does all radiation glow green and mutates people on contact?
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What ratio of bicarb to sugarcane juice with a pH level of 4.5-5.5 to neutralize pH level? [closed]
I am thinking of adding baking soda to sugarcane juice to eliminate the fruity acid that is present. The pH of sugarcane juice ranges from 4.5-5.5. I wonder how much baking soda should I incorporate ...
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Why do chiral biological molecules only exist as one enantiomer? Does it have any advantage?
Why is it that chiral biological molecules are enantiomerically pure? The other enantiomer would have the same reactivity, and the only difference is their angle of rotation of plane polarized light. ...
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Kolmogorov backward equations in active biological systems
I am trying to understand the following equations from a paper by Wang et al. [1, p. 5 at the SI]:
Michaelis–Menten Representation of the Kinesin Cycle
We assumed that there is a strong coupling ...
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How do cells form a solid structure? [closed]
How do cells unite to form a solid structure. For example a plant body is made up of a number of cells. The cells are not solid structures. Their consistency is in between solid and plasma. So how ...
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What provides the energy allowing membrane proteins to facilitate diffusion across the membrane?
We know that facilitated diffusion requires no energy. But the transport proteins, when bind to a molecule from ECF (extra-cellular face) , the proteins rotate and deliver the molecule into ICF (...
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Nomenclature of carbohydrates
In the chapter on Biomolecules in my book, the following points are given regarding carbohydrates.
Numbering the C-chain with consecutive rank
The C-atom present in the aldehyde group of aldoses and ...
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What do cannabinioids have in common structurally?
I'm looking at the wikipedia page for cannabinioids, and trying to find structural similarities between them. For plant based ones it's hard enough, the only similarity I could find seemed to be 6 ...
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Why does the structure of haemoglobin change when the ferrous ion changes to ferric ion?
It is said that $\ce{Fe^2+}$ can bind oxygen while $\ce{Fe^3+}$ cannot. Why is that so? $\ce{Fe^3+}$ has an extra electron, it could bind more easily to the oxygen. And how and why does the structure ...
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Ester vs ether links: Why are archaeal cell membranes more resistant to high temperatures and acidity than bacterial and eukaryotic membranes?
The phospholipids composing the cell membranes of eukaryotes and bacteria contain ester links between the glicerol and the fatty acids. Archaeal membranes, instead, are composed of phospholipids ...
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How to dock aggregated structures comprised of "elementary" protein units like LEGO pieces?
There are proteins with intrinsic symmetries. For example:
I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
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Biomolecular energy functions and entropy
From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
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Why there are just two Ramachandran angles in protein structure for two peptide bonds?
I really want to understand why there are just two ramachandran angles to understand the structure of the protein and why not three or many ? Can someone suggest some reference and explain this ?
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How to determine the dimensions of a bixin molecule?
I need the dimension of a bixin molecule. I do not know where to look or how to calculate this information.
I understand that this molecule has several rotational axes and conformation, so there is ...
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How to measure distance along solvent-accessible surface of protein complex in PDB file?
I am looking for a straightforward way to measure the distance between two active sites in a protein complex (PDB file).
I need the distance along the solvent-accessible surface of the protein and not ...
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Is DNA a base inside the cell?
DNA is deoxyribonucleic acid because it has phosphate groups in every one of it's nucleotides.
However, in aqueous solutions protons will ionize, leaving phosphates alone as negative groups, i.e., ...
user25327
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Why energy of some intermediates of glycolysis increases?
It is possible that I do not understand the concept of energy, but according to the diagram in my book, the energy between steps 4 and 5 and between 6 and 8 increases. How is this possible? Also, as ...
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What is the chemical formula for snake venom?
I haven't been able to get this question answered through the internet so far, so I was looking for a more professional angle in which this question can be answered.
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Can Isopropyl β-D-1-thiogalactopyranoside be degraded into either 1-deoxy-galactose or just galactose?
This may be a silly question, but is it feasible that Isopropyl β-D-1-thiogalactopyranoside (IPTG) when acted upon by a beta-galactosidase could produce 1-deoxy-galactose or just galactose?
The ...
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Comparing magnesium ion sensitivity in ribosomes to sensitivity in double-stranded DNA
I was doing some reading on this, and $\ce{Mg^2+}$ has a much greater sensitivity to ribosomes than to dsDNA (double-stranded DNA). It seems the best answer I can think of it that $\ce{Mg^2+}$ ...
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What happened to mesoporous materials for drug delivery?
A review on the topic can be found here: Wang, S. Ordered mesoporous materials for drug delivery. Microporous Mesoporous Mater. 2009, 117 (1–2), 1–9. DOI: 10.1016/j.micromeso.2008.07.002.
So the 21st ...
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What makes heat resistant proteins heat resistant?
We were doing the chapter Biomolecules in class the other day, and a doubt popped up once we reached the section on proteins.
We were taught that the stuff that keeps proteins together are: Ionic ...
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When DNA degrades, does any chemical environment preserve sequence information?
Small bits of DNA information can be found in ancient remains. In analogy to
old bones becoming mineralized, is there a chemical environment in which the
nucleic acid sequence of the original strand ...
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Does quantum mechanics play a role in protein folding?
Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. However, for the initial micro-steps of folding, when an atom, or a configuration of atoms, can ...
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Chondroitin Sulfate (greater volume in solution than in crystal form)
I've read in a textbook on biophysics that chondroitin sulfate occupies a greater volume in a solution than in crystalline form. Why is that?
Is it because of hydrogen bonds in solution that the ...
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What are some of the more easily manipulated residues on an enzyme?
I am trying to attach a cross-linker to an enzyme and I am looking for candidates for reaction sites. I have several amino acids that are present on the surface of the enzyme (hydrophilic) but I am ...
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