ChargeCalculator:Case studies - Revision history

Crina: /* Proteasome */

2015-06-14T19:14:47Z

Proteasome

← Older revision		Revision as of 19:14, 14 June 2015
Line 27:		Line 27:
	<br style="clear:both" />		<br style="clear:both" />

	=~~Proteasome~~=		=Paracetamol – atomic charges and allostery of large biomacromolecular complexes=
	The 20S subunit is the catalytic machinery of proteasomes, whose main function is to break down unneeded or damaged proteins. The 20S proteasome is a cylindrical nanoparticle with a wide hollow core, where protein degradation takes place at multiple catalytic sites. The proteolysis mechanism is enabled by a threonine-dependent nucleophilic attack, which may depend on associated water molecules for deprotonation of the reactive threonine hydroxyl. It is possible to study the influence of water molecules on the charge distribution of the catalytic threonine before moving on to more complex modeling studies of the catalytic reaction itself.

	~~There are 7 beta catalytic units in the 20s~~ proteasome~~, each~~ made up of ~~two chains (H-N,V-Z,1,2)~~. ~~The catalytic THR residues occupy~~ the ~~N-terminal position of each chain, so its residue serial number will be 1~~, and ~~we expect it to~~ be ~~positively charged. In eukariotes, only 4 of these beta subunits contain~~ the ~~expected catalytic THR residues (chains H,I,L,N,V,W,Z,2)~~.		[[File:Proteasome.png\|thumb\|right\|650px\|The 26S proteasome is a large machine consisting of a regulatory particle and a core particle. The core particle is made up of alpha and beta rings. Information pertaining to allosteric regulation travels across the proteasome in a vertical and horizontal fashion, and can be traced based on the change in total charge between different conformational states.]]

	~~For studying~~ the ~~potential influence~~ of ~~water on~~ the catalytic ~~THR~~, ~~we have calculated atomic charges for~~ the ~~20S~~ proteasome of ~~cattle~~ (~~PDB ID 1IRU~~) ~~using an EEM parameter set specifically developed for proteins~~, ~~since~~ the ~~20S proteasome is actually a large complex of multiple proteins~~. ~~Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/cdfa7d75-a660-45bf-b263-b92e0f880f73?example=Proteasome here]~~, ~~and make sure~~ to ~~use~~ the ~~interactive guides for additional explanations~~.		The 26S proteasome is a large biomacromolecular complex which facilitates the targeted degradation of intracellular proteins, and thus plays an essential role in keeping protein homeostasis. It consists of a core particle, made up of alpha rings and beta rings, controlled by regulatory particles, which are made up of a number of proteins. The proteasome is an intricate molecular machine which requires complex regulation to unfold and deubiquityilate the substrate, and push it through the catalytic machinery located in the beta rings. Necessarily, the proteasome undergoes large conformational changes during its operation. However, due to its size, such changes are very difficult to study. Recent work in the field of cryo-electron microscopy has lead to the discovery of intermediate conformers during the initial binding of ubiquitylated substrates. While the conformational changes in the regulatory particle are easily distinguishable (average backbone atom RMSD 10.4 Å), the changes in the core particle are very subtle (average backbone atom RMSD 1.5 Å), due to the fact that all studied conformers refer to the initial phase of substrate binding.

	The results ~~of the calculation~~ are available [http://~~webchemdev.~~ncbr.muni.cz/~~Platform~~/~~ChargeCalculator/Result~~/Proteasome~~/proteasome-water-ions here~~].		Using ACC, we calculated atomic charges in these 3 intermediate conformers of the 26S proteasome that are available in the Protein Data Bank (PDB IDs: 4CR2, 4CDR3, 4CR4). The default ACC settings were used. The computation took 130s, and the complete results are available [http://ncbr.muni.cz/ACC/CaseStudy/Proteasome on the ACC web page].

	The ~~presence~~ of ~~water molecules generally makes~~ the ~~catalytic THR residues less positive by up to 0~~.~~08e. This effect~~ is ~~favorable to the catalytic activity~~, ~~as the THR hydrogen~~ is ~~partially drawn~~ to ~~water~~, ~~enabling~~ the ~~reactive hydroxyl~~ to ~~initiate the nucleophilic attack~~. ~~Maximum effect is seen where water forms an H-bond with~~ the ~~THR hydroxyl (e.g., THR 1 from chain W). A smaller effect is seen where~~ the ~~water is not in optimal position to~~ form ~~an H bond (e.g~~., ~~THR~~ 1 ~~from chain V). The only exception is~~ the ~~catalytic THR of chain L~~, ~~where~~ the ~~presence of water actually seems~~ to ~~make~~ the ~~THR more positive by over 0~~.~~2e. This is caused by~~ the ~~presence~~ of ~~not one~~, ~~but three water molecules in close proximity of THR~~, and ~~is probably related to~~ the ~~different substrate specificity~~ of ~~this site~~.		The calculation produced one 3 sets of atomic charges for each conformer of the 26S proteasome. Since the proteasome is very large, it is difficult to draw conclusions based only on atomic or even residue charges. To obtain the total charge for a specific subunit or even entire particle, just sum up all the atomic charges for atoms which belong to that subunit or particle. Subunit information can be found in the input file in the form of chains. Thus, atoms with the chain identifier 1-7 belong to the beta ring, A-G belong to the alpha ring, and H-Z belong to the regulatory particle. By comparing the total charge of each particle or subunit across the conformational state 1 (PDB ID: 4CR2), state 2 (PDB ID: 4CR3), and state 3 (PDB ID: 4CR4), conclusions can be drawn regarding the direction of information flow inside the proteasome.

	~~Note~~ that the ~~input file also contains Mg ions~~, ~~which were probably used~~ to ~~stabilize the 20S proteasome in the original experiment that produced the structure with PDB ID 1iru. The influence~~ of ~~Mg ions on~~ the ~~catalytic THR can also be studied in~~ the ~~same straightforward fashion as above~~. ~~Simply remove the ions from~~ the ~~input file~~, ~~run ACC~~ with the ~~same setup~~, and ~~then compare the charge on~~ the ~~catalytic THR residues between the two computations (with and without Mg ions)~~.		The first observation is that, during the conformational changes from state 1, to state 2, and then to state 3, a significant amount of electron density is transferred between the core particle and the regulatory particle. This suggests that, even though there is no significant movement observed for the core particle, allosteric information is exchanged with the core particle, and this information can be tracked at the electrostatic level.

	~~'''Return~~ to the [[ChargeCalculator~~:UserManual \| Table~~ of ~~contents]]~~.~~'''~~		The next observation is that significant information is disseminated not only horizontally (within the alpha ring, or within the beta ring), but also vertically. In the overall transition it appears that the alpha ring loses electron density to the regulatory particle. By checking the intermediate state 2 it is possible to see that there is also transfer between the alpha ring and beta ring. This vertical shuttling of electron density within the catalytic core particle suggests that the activity of alpha and beta subunits may cross-correlate. Such phenomena have indeed been reported. For example, alpha5 and beta1 may translocate together, while knockdown of alpha1 leads to loss of chymotrypsin activity associated with beta5.

			Further analysis can even yield the residues involved in the allosteric regulation, as those residues which exhibit a high variation in total charge (e.g., approximately 10 sites on the Rpn-13 regulatory subunit). This case study shows how a brief calculation using only a crude structural approximation can give insight regarding allosteric regulation in large biomolecular complexes.

			You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/47a5bd67-5b9f-4138-8432-c1b9dc059b8e?example=Proteasome here], and make sure to use the interactive guides for additional explanations. We have used the default ACC settings, meaning that the total charge was 0 for all conformers, the EEM parameter set covers NPA atomic charges at the HF/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.
			<br style="clear:both" />

Crina: /* Protegrin-1 – atomic charges and activity of antimicrobial peptides */

2015-06-14T18:21:33Z

Protegrin-1 – atomic charges and activity of antimicrobial peptides

← Older revision		Revision as of 18:21, 14 June 2015
Line 16:		Line 16:
	=Protegrin-1 – atomic charges and activity of antimicrobial peptides=		=Protegrin-1 – atomic charges and activity of antimicrobial peptides=

	[[File:Protegrin.png\|thumb\|right\|300px\| ~~Each residue position is~~ represented by ~~a sphere~~ colored ~~according to the~~ residue ~~charge~~. ~~The size is proportional to the absolute charge. The ARG residues at positions 4~~ and 9 are significantly less positive than the rest of the ARG residues, indicating that mutations at these positions may be less effective.]]		[[File:Protegrin.png\|thumb\|right\|300px\| Residue centroids represented by spheres colored by residue charges. Residues ARG4 and ARG9 are significantly less positive (lighter blue) than the rest of the ARG residues (darker blue), indicating that mutations at these positions may be less effective.]]

	Protegrins are a family of antimicrobial peptides active against a wide range of pathogens. Protegrin-1 (PG1) has been intensely studied for its potential in treating infections caused by antibiotic resistant bacteria. PG1 shows activity against several pathogens, but also toxicity against the host. Useful mutations are those which maintain the antimicrobial activity, and at the same time reduce toxicity.		Protegrins are a family of antimicrobial peptides active against a wide range of pathogens. Protegrin-1 (PG1) has been intensely studied for its potential in treating infections caused by antibiotic resistant bacteria. PG1 shows activity against several pathogens, but also toxicity against the host. Useful mutations are those which maintain the antimicrobial activity, and at the same time reduce toxicity.
Line 25:		Line 25:

	You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/dc41612f-b3c0-4207-97a6-b70598e90d88?example=Protegrin here], and make sure to use the interactive guides for additional explanations. The total molecular charge was +7, owing to the many ARG residues. The EEM parameter set used was EX-NPA_6-31Gd_gas, but it was necessary to add to this set EEM parameters for deuterium (D), because this element was present in the input file. The EEM parameters for D were identical to the parameters for H. The EEM parameter set covers NPA atomic charges at the HF/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. The rest of the ACC default settings were kept.		You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/dc41612f-b3c0-4207-97a6-b70598e90d88?example=Protegrin here], and make sure to use the interactive guides for additional explanations. The total molecular charge was +7, owing to the many ARG residues. The EEM parameter set used was EX-NPA_6-31Gd_gas, but it was necessary to add to this set EEM parameters for deuterium (D), because this element was present in the input file. The EEM parameters for D were identical to the parameters for H. The EEM parameter set covers NPA atomic charges at the HF/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. The rest of the ACC default settings were kept.
			<br style="clear:both" />

	=Proteasome=		=Proteasome=

Crina: /* Paracetamol – atomic charges and chemical reactivity in small drug like molecules */

2015-06-14T18:18:55Z

Paracetamol – atomic charges and chemical reactivity in small drug like molecules

← Older revision		Revision as of 18:18, 14 June 2015
Line 12:		Line 12:

	You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/8ed40f3c-48e7-4a1d-9d86-7ec541c95984?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used the default ACC settings, meaning that the total charge was 0, the EEM parameter set covers NPA atomic charges at the B3LYP/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.		You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/8ed40f3c-48e7-4a1d-9d86-7ec541c95984?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used the default ACC settings, meaning that the total charge was 0, the EEM parameter set covers NPA atomic charges at the B3LYP/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.
			<br style="clear:both" />

	=Protegrin-1 – atomic charges and activity of antimicrobial peptides=		=Protegrin-1 – atomic charges and activity of antimicrobial peptides=

Crina: /* Apoptosis */

2015-06-14T18:09:56Z

Apoptosis

← Older revision		Revision as of 18:09, 14 June 2015
Line 13:		Line 13:
	You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/8ed40f3c-48e7-4a1d-9d86-7ec541c95984?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used the default ACC settings, meaning that the total charge was 0, the EEM parameter set covers NPA atomic charges at the B3LYP/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.		You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/8ed40f3c-48e7-4a1d-9d86-7ec541c95984?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used the default ACC settings, meaning that the total charge was 0, the EEM parameter set covers NPA atomic charges at the B3LYP/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.

	=~~Apoptosis=~~		=Protegrin-1 – atomic charges and activity of antimicrobial peptides=
	~~The protein Bax is important in regulating programmed cell death (apoptosis). Upon activation, Bax oligomerizes~~ and ~~causes a cascade~~ of events which eventually leads to the death of the cell. Bax activation is a transient phenomenon believed to rely on a specific network of charge transfer. The active Bax appears in complex with a charged activator peptide, causing a few conformational changes and a shift in the total charge. The distribution of charges can be studied individually, and further compared between the active and inactive states.

	For studying Bax activation we have calculated atomic charges for the active (PDB ID 2k7w) and inactive (PDB ID 1f16) forms of Bax using an EEM parameter set specifically developed for proteins. Try out this particular computation setup [~~http~~:~~//webchemdev~~.~~ncbr~~.~~muni~~.~~cz/Platform/ChargeCalculator/Result/8d5e4fb1-5471-4a91-99a8-624cce2c596a?example=Apoptosis here],~~ and ~~make sure to use~~ the ~~interactive guides for additional explanations. Note that~~ the ~~input files were in pqr format~~, ~~and contained AMBER charges as given by the program pdb2pqr. These are also available for comparison in ACC~~.		[[File:Protegrin.png\|thumb\|right\|300px\| Each residue position is represented by a sphere colored according to the residue charge. The size is proportional to the absolute charge. The ARG residues at positions 4 and 9 are significantly less positive than the rest of the ARG residues, indicating that mutations at these positions may be less effective.]]

	~~The results~~ of ~~the calculation are available [http://webchemdev~~.~~ncbr~~.~~muni~~.~~cz/Platform/ChargeCalculator/Result/Bax here]~~.		Protegrins are a family of antimicrobial peptides active against a wide range of pathogens. Protegrin-1 (PG1) has been intensely studied for its potential in treating infections caused by antibiotic resistant bacteria. PG1 shows activity against several pathogens, but also toxicity against the host. Useful mutations are those which maintain the antimicrobial activity, and at the same time reduce toxicity.

	~~EEM allows inter-residue polarization and charge transfer, and thus the total residue~~ charges ~~given by EEM will deviate from the formal values of +1,0 and -1, respectively~~. The ~~total residue charges given by AMBER always coincide with the formal values, as they do not account for~~ the ~~influence of~~ the ~~surrounding environment. A number of residues~~ in the ~~inactive Bax deviate~~ from the ~~formal charge~~, ~~suggesting electrostatically interesting sites. Most~~ are on the ~~surface of Bax, but some are also inside the protein (e~~.g.~~, ARG 109)~~.		We calculated atomic charges in PG1 using ACC. The geometry of the PG1 molecule corresponded to the lowest energy NMR model in the entry 1PG1 (PDB: 1PG1) from the Protein Data Bank. The computation took less than 1s, and the complete results are available on the [http://ncbr.muni.cz/ACC/CaseStudy/Protegrin ACC web page].

	~~Further~~, we ~~can compare~~ the ~~total~~ residue charges ~~between active and inactive Bax~~. ~~For instance~~, the ~~residue~~ ARG ~~109 has a~~ charge of +0.~~07e in inactive Bax~~, ~~and~~ +0.~~37e in active Bax~~. ~~This significant difference may be~~ a ~~clue that this~~ residue ~~is relevant during activation. Indeed,~~ a ~~triple mutant~~ at positions ~~109-111 shows decreased biological activity~~.		The calculation produced one set of atomic charges. PG1 contains 18 residues, and rather than analyzing atomic charges, we analyzed the residue charges, which are also reported by ACC (Figure 4B). PG1 is special because of its high positive charge. It contains 6 ARG residues. However, not all have the same charge. In particular, ARG at positions 4 and 9 have the least positive charge (around +0.5e), whereas the rest have much higher positive charge (over +0.8e). Such results suggest that mutations of ARG into a neutral residue at positions 4 or 9 would have a lower effect than mutations at positions 1, 10, 11 or 18. This seems to be indeed the case, as it was found that the mutation of ARG 4 alters the antimicrobial activity against C. albicans significantly less than the mutation of ARG 10. Such biologically relevant insight can be gained by analyzing the residue charges on a single structure of PG1.

	~~Note again~~ that the ~~absolute values~~ of the ~~charges are not always relevant~~. ~~But~~ the ~~trends within a certain set~~ of charges ~~can hold~~ a ~~lot~~ of ~~relevant information~~. ~~Moreover~~, ~~not all~~ charge ~~differences may be of interest~~. ~~For instance~~, ~~when comparing between~~ the ~~values~~ for ~~highly flexible parts of~~ the ~~protein,~~ the ~~noise (differences caused by entirely different conformation~~ and ~~hence chemical environment) can be higher than~~ the ~~information content. Thus, context is always important~~.		You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/dc41612f-b3c0-4207-97a6-b70598e90d88?example=Protegrin here], and make sure to use the interactive guides for additional explanations. The total molecular charge was +7, owing to the many ARG residues. The EEM parameter set used was EX-NPA_6-31Gd_gas, but it was necessary to add to this set EEM parameters for deuterium (D), because this element was present in the input file. The EEM parameters for D were identical to the parameters for H. The EEM parameter set covers NPA atomic charges at the HF/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. The rest of the ACC default settings were kept.

	=Proteasome=		=Proteasome=

Crina: /* Paracetamol */

2015-06-14T17:50:57Z

Paracetamol

← Older revision		Revision as of 17:50, 14 June 2015
Line 1:		Line 1:
	We present a few interesting examples of use cases for '''ACC'''.		We present a few interesting examples of use cases for '''ACC'''.

	=Paracetamol=		=Paracetamol – atomic charges and chemical reactivity in small drug like molecules=
	~~N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic~~ and ~~antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-inflammatory compounds. In order to study the interaction of the~~ drug ~~with its target, it is necessary to look at the electrostatic properties of paracetamol. Further modeling studies will also require atomic charges for paracetamol as parameters of the simulation.~~

	~~We have computed atomic charges in paracetamol (experimental coordinates from wwPDB CCD). Try out this particular computation setup~~ [~~http~~:~~//webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/0d51e6ec-8f80-4dbf-af10-79bdd07ec368?example=~~Paracetamol ~~here], and make sure to use the interactive guides for additional explanations~~. ~~We have used two EEM parameter sets available~~ in ~~literature, which cover two atomic charge definitions at~~ the B3LYP/6-31G* level of theory. MK charges are more likely to give good electrostatic potentials, whereas NPA charges generally support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to ~~use charges which are compatible with~~ the ~~particular force field you plan to use. For instance, if~~ the ~~force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition~~.		[[File:Paracetamol.png\|thumb\|right\|650px\|The most positive H in the paracetamol molecule correspond to the most reactive sites during the metabolic degradation of paracetamol.]]

	~~The results~~ of the ~~calculation are available [http://webchem~~.~~ncbr.muni.cz/Platform/ChargeCalculator/Result/Paracetamol/~~paracetamol ~~here]~~.		N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic and antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-inflammatory compounds. The metabolic break down of paracetamol has been the subject of intense study, since it holds the key to both its therapeutic action and toxicity.

	The ~~phenolic H appears to be the most positive H in~~ the paracetamol molecule~~. The H bound~~ to the ~~amide N is~~ the ~~second most positive H~~. ~~Not surprisingly~~, ~~these positions represent~~ the ~~reaction sites for all metabolic modifications of paracetamol~~. ~~While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules~~.		We calculated atomic charges in paracetamol using ACC. The geometry of the paracetamol molecule corresponded to the ideal coordinates for the entry TYL from the wwPDB Chemical Compounds Database (wwPDB CCD: TYL). The default ACC settings were used. The computation took less than 1s, and the complete results are available on the [http://ncbr.muni.cz/ACC/CaseStudy/Paracetamol ACC web page].

	~~Different EEM parameter sets produce~~ a ~~range~~ of ~~absolute values for the atomic charges~~. ~~For instance~~, ~~in our calculation~~ the phenolic H in paracetamol ~~has an MK charge of +0~~.~~31e~~, and ~~an NPA~~ charge ~~of +~~0~~.42e. While~~ the ~~main trends observed within each~~ set of charges ~~hold true~~, these ~~values cannot be compared between sets~~, ~~due~~ to the ~~inherently different nature of~~ the ~~charge definitions they are~~ based on~~. On the other hand~~, ~~these differences might allow~~ one set ~~of charges to sample conformations not accessible to other sets~~.		A quick analysis reveals that the phenolic H (position HO4) is the most acidic proton (highest positive charge) in the molecule, suggesting a faster and easier dissociation of this O-H bond. Indeed up to 90% of metabolic degradation happens at position HO4 (glucunronidationration, sulphonation). Additionally, up to 15% of metabolic degradation involves dehydrogenation oxidation at the phenolic (HO4) and amidic positions (HN), the two most positive H in the paracetamol molecule. While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules.

			You can try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/8ed40f3c-48e7-4a1d-9d86-7ec541c95984?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used the default ACC settings, meaning that the total charge was 0, the EEM parameter set covers NPA atomic charges at the B3LYP/6-31G* level of theory. These charges are expected to support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.

	=Apoptosis=		=Apoptosis=

Crina: /* Paracetamol */

2014-12-24T06:49:25Z

Paracetamol

← Older revision		Revision as of 06:49, 24 December 2014
Line 4:		Line 4:
	N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic and antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-inflammatory compounds. In order to study the interaction of the drug with its target, it is necessary to look at the electrostatic properties of paracetamol. Further modeling studies will also require atomic charges for paracetamol as parameters of the simulation.		N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic and antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-inflammatory compounds. In order to study the interaction of the drug with its target, it is necessary to look at the electrostatic properties of paracetamol. Further modeling studies will also require atomic charges for paracetamol as parameters of the simulation.

	We have computed atomic charges in paracetamol (experimental coordinates from wwPDB CCD). Try out this particular computation setup [http://~~webchemdev~~.ncbr.muni.cz/Platform/ChargeCalculator/Result/~~bbb36e26~~-~~f807~~-~~4bf4~~-~~bf88~~-~~0cda9e5cd20d~~?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used ~~several~~ EEM parameter sets available in literature, ~~in order~~ to ~~cover~~ a ~~wide range of atomic~~ charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.		We have computed atomic charges in paracetamol (experimental coordinates from wwPDB CCD). Try out this particular computation setup [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/0d51e6ec-8f80-4dbf-af10-79bdd07ec368?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used two EEM parameter sets available in literature, which cover two atomic charge definitions at the B3LYP/6-31G* level of theory. MK charges are more likely to give good electrostatic potentials, whereas NPA charges generally support qualitative chemical concepts like induction and conjugation. In general, it is a good idea to try several charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.

	The results of the calculation are available [http://~~webchemdev~~.ncbr.muni.cz/Platform/ChargeCalculator/Result/Paracetamol/paracetamol here].		The results of the calculation are available [http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/Result/Paracetamol/paracetamol here].

	The phenolic H appears to be ~~not only~~ the most positive H in the paracetamol molecule~~, but also the second most positive atom in the entire molecule (the most positive is the amide C)~~. The H bound to the amide N is the second most positive H~~, and the third most positive atom in the entire molecule~~. Not surprisingly, these positions represent the reaction sites for all metabolic modifications of paracetamol. While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules.		The phenolic H appears to be the most positive H in the paracetamol molecule. The H bound to the amide N is the second most positive H. Not surprisingly, these positions represent the reaction sites for all metabolic modifications of paracetamol. While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules.

	Different EEM parameter sets produce a range of absolute values for the atomic charges. For instance, ~~the atomic charge on~~ the phenolic H in paracetamol ~~may be anywhere between~~ +0.1e and +0.~~34e, depending on which EEM parameter set was used~~. While the trends observed within each set of charges hold true, these values cannot be compared between sets, due to the inherently different nature of the charge definitions they are based on. On the other hand, these differences might allow one set of charges to sample conformations not accessible to other sets.		Different EEM parameter sets produce a range of absolute values for the atomic charges. For instance, in our calculation the phenolic H in paracetamol has an MK charge of +0.31e, and an NPA charge of +0.42e. While the main trends observed within each set of charges hold true, these values cannot be compared between sets, due to the inherently different nature of the charge definitions they are based on. On the other hand, these differences might allow one set of charges to sample conformations not accessible to other sets.

	=Apoptosis=		=Apoptosis=

Crina: /* Proteasome */

2014-12-08T15:18:47Z

Proteasome

← Older revision		Revision as of 15:18, 8 December 2014
Line 30:		Line 30:
	There are 7 beta catalytic units in the 20s proteasome, each made up of two chains (H-N,V-Z,1,2). The catalytic THR residues occupy the N-terminal position of each chain, so its residue serial number will be 1, and we expect it to be positively charged. In eukariotes, only 4 of these beta subunits contain the expected catalytic THR residues (chains H,I,L,N,V,W,Z,2).		There are 7 beta catalytic units in the 20s proteasome, each made up of two chains (H-N,V-Z,1,2). The catalytic THR residues occupy the N-terminal position of each chain, so its residue serial number will be 1, and we expect it to be positively charged. In eukariotes, only 4 of these beta subunits contain the expected catalytic THR residues (chains H,I,L,N,V,W,Z,2).

	For studying the potential influence of water on the catalytic THR, we have calculated atomic charges for the 20S proteasome of cattle (PDB ID 1IRU) using an EEM parameter set specifically ~~developped~~ for proteins, since the 20S proteasome is actually a large complex of multiple proteins. Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/cdfa7d75-a660-45bf-b263-b92e0f880f73?example=Proteasome here], and make sure to use the interactive ~~giudes~~ for additional explanations.		For studying the potential influence of water on the catalytic THR, we have calculated atomic charges for the 20S proteasome of cattle (PDB ID 1IRU) using an EEM parameter set specifically developed for proteins, since the 20S proteasome is actually a large complex of multiple proteins. Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/cdfa7d75-a660-45bf-b263-b92e0f880f73?example=Proteasome here], and make sure to use the interactive guides for additional explanations.

	The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Proteasome/proteasome-water-ions here].		The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Proteasome/proteasome-water-ions here].

Crina: /* Apoptosis */

2014-12-08T15:18:11Z

Apoptosis

← Older revision		Revision as of 15:18, 8 December 2014
Line 13:		Line 13:

	=Apoptosis=		=Apoptosis=
	The protein Bax is important in regulating programmed cell death (apoptosis). Upon activation, Bax oligomerizes and causes a cascade of events which eventually leads to the death of the cell. Bax activation is a transient phenomenon believed to rely on a specific network of charge transfer. The active Bax appears in complex with a charged activator peptide, causing a few conformational changes and a shift in the total charge. The distribution of charges can be studied individually, and ~~furhter~~ compared between the active and inactive states.		The protein Bax is important in regulating programmed cell death (apoptosis). Upon activation, Bax oligomerizes and causes a cascade of events which eventually leads to the death of the cell. Bax activation is a transient phenomenon believed to rely on a specific network of charge transfer. The active Bax appears in complex with a charged activator peptide, causing a few conformational changes and a shift in the total charge. The distribution of charges can be studied individually, and further compared between the active and inactive states.

	For studying Bax activation we have calculated atomic charges for the active (PDB ID 2k7w) and inactive (~~pdb id~~ 1f16) forms of ~~bax~~ using an ~~eem~~ parameter set specifically ~~developped~~ for proteins. Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/8d5e4fb1-5471-4a91-99a8-624cce2c596a?example=Apoptosis here], and make sure to use the interactive ~~giudes~~ for additional explanations. Note that the input files were in pqr format, and contained AMBER charges as given by the program pdb2pqr. These are also available for comparison in ACC.		For studying Bax activation we have calculated atomic charges for the active (PDB ID 2k7w) and inactive (PDB ID 1f16) forms of Bax using an EEM parameter set specifically developed for proteins. Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/8d5e4fb1-5471-4a91-99a8-624cce2c596a?example=Apoptosis here], and make sure to use the interactive guides for additional explanations. Note that the input files were in pqr format, and contained AMBER charges as given by the program pdb2pqr. These are also available for comparison in ACC.

	The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Bax here].		The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Bax here].

Crina: /* Paracetamol */

2014-12-08T15:15:40Z

Paracetamol

← Older revision		Revision as of 15:15, 8 December 2014
Line 2:		Line 2:

	=Paracetamol=		=Paracetamol=
	N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic and antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-~~inflamatory~~ compounds. In order to study the interaction of the drug with its target, it is necessary to look at the electrostatic properties of paracetamol. Further modeling studies will also require atomic charges for paracetamol as parameters of the simulation.		N-acetyl-p-aminophenol, commonly known as paracetamol, is a widely used analgesic and antipyretic. Its mechanism of action is believed to be the inhibition of the protein cyclooxygenase 2, regulating the production of pro-inflammatory compounds. In order to study the interaction of the drug with its target, it is necessary to look at the electrostatic properties of paracetamol. Further modeling studies will also require atomic charges for paracetamol as parameters of the simulation.

	We have computed atomic charges in paracetamol (experimental coordinates from wwPDB CCD). Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/bbb36e26-f807-4bf4-bf88-0cda9e5cd20d?example=Paracetamol here], and make sure to use the interactive ~~giudes~~ for additional explanations. We have used several EEM parameter sets available in literature, in order to cover a wide range of atomic charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.		We have computed atomic charges in paracetamol (experimental coordinates from wwPDB CCD). Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/bbb36e26-f807-4bf4-bf88-0cda9e5cd20d?example=Paracetamol here], and make sure to use the interactive guides for additional explanations. We have used several EEM parameter sets available in literature, in order to cover a wide range of atomic charge definitions. One or more of these might prove useful in further modeling studies. If you plan to run molecular dynamics, it is good to use charges which are compatible with the particular force field you plan to use. For instance, if the force field is known to use atomic charges based on electrostatic potential mapping, pick at least one EEM parameter set developed with this charge definition.

	The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Paracetamol/paracetamol here].		The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Paracetamol/paracetamol here].
Line 10:		Line 10:
	The phenolic H appears to be not only the most positive H in the paracetamol molecule, but also the second most positive atom in the entire molecule (the most positive is the amide C). The H bound to the amide N is the second most positive H, and the third most positive atom in the entire molecule. Not surprisingly, these positions represent the reaction sites for all metabolic modifications of paracetamol. While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules.		The phenolic H appears to be not only the most positive H in the paracetamol molecule, but also the second most positive atom in the entire molecule (the most positive is the amide C). The H bound to the amide N is the second most positive H, and the third most positive atom in the entire molecule. Not surprisingly, these positions represent the reaction sites for all metabolic modifications of paracetamol. While paracetamol is a very small molecule with few polar sites, the same principle can be applied in reasoning out highly reactive sites in more complex molecules.

	Different EEM parameter sets produce a range of absolute values for the atomic charges. For instance, the phenolic H in paracetamol may ~~have~~ anywhere between +0.1e and +0.34e, depending on which EEM parameter set was used. While the trends observed within each set of charges hold true, these values cannot be compared between sets, due to the inherently different nature of the charge definitions they are based on. On the other hand, these differences might allow one set of charges to sample conformations not accessible to other sets.		Different EEM parameter sets produce a range of absolute values for the atomic charges. For instance, the atomic charge on the phenolic H in paracetamol may be anywhere between +0.1e and +0.34e, depending on which EEM parameter set was used. While the trends observed within each set of charges hold true, these values cannot be compared between sets, due to the inherently different nature of the charge definitions they are based on. On the other hand, these differences might allow one set of charges to sample conformations not accessible to other sets.

	=Apoptosis=		=Apoptosis=

Crina: /* Proteasome */

2014-11-29T04:16:37Z

Proteasome

← Older revision		Revision as of 04:16, 29 November 2014
Line 30:		Line 30:
	There are 7 beta catalytic units in the 20s proteasome, each made up of two chains (H-N,V-Z,1,2). The catalytic THR residues occupy the N-terminal position of each chain, so its residue serial number will be 1, and we expect it to be positively charged. In eukariotes, only 4 of these beta subunits contain the expected catalytic THR residues (chains H,I,L,N,V,W,Z,2).		There are 7 beta catalytic units in the 20s proteasome, each made up of two chains (H-N,V-Z,1,2). The catalytic THR residues occupy the N-terminal position of each chain, so its residue serial number will be 1, and we expect it to be positively charged. In eukariotes, only 4 of these beta subunits contain the expected catalytic THR residues (chains H,I,L,N,V,W,Z,2).

	For studying the potential influence of water on the catalytic THR, we have calculated atomic charges for the 20S proteasome of cattle (PDB ID 1IRU) using an EEM parameter set specifically developped for proteins, since the 20S proteasome is actually a large complex of multiple proteins.		For studying the potential influence of water on the catalytic THR, we have calculated atomic charges for the 20S proteasome of cattle (PDB ID 1IRU) using an EEM parameter set specifically developped for proteins, since the 20S proteasome is actually a large complex of multiple proteins. Try out this particular computation setup [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/cdfa7d75-a660-45bf-b263-b92e0f880f73?example=Proteasome here], and make sure to use the interactive giudes for additional explanations.

			The results of the calculation are available [http://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator/Result/Proteasome/proteasome-water-ions here].

	The presence of water molecules generally makes the catalytic THR residues less positive by up to 0.08e. This effect is favorable to the catalytic activity, as the THR hydrogen is partially drawn to water, enabling the reactive hydroxyl to initiate the nucleophilic attack. Maximum effect is seen where water forms an H-bond with the THR hydroxyl (e.g., THR 1 from chain W). A smaller effect is seen where the water is not in optimal position to form an H bond (e.g., THR 1 from chain V). The only exception is the catalytic THR of chain L, where the presence of water actually seems to make the THR more positive by over 0.2e. This is caused by the presence of not one, but three water molecules in close proximity of THR, and is probably related to the different substrate specificity of this site.		The presence of water molecules generally makes the catalytic THR residues less positive by up to 0.08e. This effect is favorable to the catalytic activity, as the THR hydrogen is partially drawn to water, enabling the reactive hydroxyl to initiate the nucleophilic attack. Maximum effect is seen where water forms an H-bond with the THR hydroxyl (e.g., THR 1 from chain W). A smaller effect is seen where the water is not in optimal position to form an H bond (e.g., THR 1 from chain V). The only exception is the catalytic THR of chain L, where the presence of water actually seems to make the THR more positive by over 0.2e. This is caused by the presence of not one, but three water molecules in close proximity of THR, and is probably related to the different substrate specificity of this site.