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- Enzymatic reaction without amino acid residues' participation?
I am a beginner in computational chemistry. And I have a problem now with modelling an enzymatic reaction. I tried to cut part of the catalytic pocket as a cluster model and succeeded to locate the transition state. The transition state has been verified with frequency analysis. But the problem is that it seems that no amino acid residue participates in the reaction. Is this reasonable? I am afraid that this problem is because I freezed some alpha C atoms. Do you have any idea on this?
Sometimes the main role of the catalytic site is to lock the substrate(s) in a "reactive" conformation. And if the C alphas are relatively far away from the reactant (e.g., no h-bonding with the backbone), freezing should be ok if the starting geometry favors the reaction.
Anyway, since the electrostatic environment can be relevant for the reaction, it is often convenient to use a QM/MM scheme, and start with a classical MD simulation of the whole system to look at the dynamics of the protein-ligand complex. Then you can see for yourself if any protein residues are likely to directly partake in the reaction.
Of course this is quite tedious, and the improvement might be negligible depending on your system. But without further knowledge, it's hard to tell whether or not your model is missing any key features, even though the approach you're using isn't inherently flawed.Following
- Can someoe suggest me some thixotropic agents?
I've commercially available UV curable, acrylated urethane based adhesives, their viscosity is about 6000 cP while I want to increase it upto 30,000 or more. Sould I need more UV curable resin to these adhesives after adding thixotropic agent?
Yes, hydrophobic Fumed silica works good...Following
- Is it necessary to have bilingual experts (with formal education) for translating a questionnaire?
While testing a questionnaire for its validation and cross-cultural adaptation, is it necessary to have bilingual experts with formal education? E.g translation of Nordic questionnaire into Urdu (is it necessary that the translators have a formal level of education/degree in Urdu or English?)
Could it be done by someone who is brilliant at both languages but does not have formal education?
Secondly, how is the sample size selected for translation-based studies like this? Inclusion and exclusion criteria and number of participants etc...
Thanks in anticipation.
Thank you for your responses. What about sample selection in these studies? Sample size, inclusion and exclusion criteria etc?
Let's consider a scale with eight (8) items, how much would the sample size be for it? 5 participants per item or more?
Additionally, is it necessary to have target population with disease/disorder if we are testing a relevant tool or it can be tested on healthy individuals?Following
- Is it time we shift emphasis from technological solutions to climate change & focus on the 'Human Dimension'?
Is it not obvious that nature can heal itself, if only left alone, and it is we humans who need regulation? Many natural parks managers do just that; seal off the area from human interference to let nature heal and recover. It is classified as 'Strict Nature Reserve"by IUCN. Complacency and inaction are not advocated here, as many have misunderstood, but the shifting of focus from technology to the human being. As technology is no match for human greed, isn't introspection & restraining ourselves more relevant than developing more technology, which caused the mess in the first place, by making it easy for a few to consume more? Since technology is only a short term quick fix which fails after a short time, isn't the real problem our addiction to material consumption & our lack of understanding about human nature? Isn't developing more technology sustaining the addiction instead of correcting it, leading to more complex problems later on, needing more complex technological quick fixes like higher drug dosages, more ground troops & equipment, (along with their debilitating side effects) in the future? Isn't this the vicious addiction circle we are trapped in? As researchers, do we merely buy more time with technology OR go to the very root of the problem, the human being?
A lot of hue and cry is made about climate change and the environment in general. Public and private money is poured into research to study its effects on the environment, sustainability etc. Should we study nature or ourselves?
" Our studies must begin with our selves and not with the heavens. "-Ouspensky
Human activities have been found to have a direct correlation to climate change and its impact on the environment(I=P x A x T, the Ehrlich and Holdren equation), in spite of what some complacent sections say to protect their own self interests.
We hardly know about Human nature. We can scarcely predict human behavior. We need to find out why we think like we do and why we do what we do and why, in spite of all knowledge and wisdom, consume more than what we need, in the form of addictions to consumption and imbalance not only ourselves but also the family, society and environment around us..
Humanity is directly responsible for all the unnatural imbalances occurring on the planet. Yet we refuse to take responsibility and instead focus on climate change, or fool the public exchequer with a 'breakthrough in renewable energy just around the corner'. We scarcely know what drives human beings. If we had known, all the imbalances around us would have had solutions by now, given the amount of money plowed into finding such solutions. Are we blindly groping in the dark of climate change because we don't know the answers to our own nature?
Is it not high time we focus on what makes us human, correct our consumptive behavior and leave nature to take care of climate change? Why focus effort on 'externals' when the problem is 'internal'- 'me'?
Aren't we addicts denying our addiction and blaming everything else but ourselves?
" We are what we Think.
All that we are arises with our thoughts.
With our thoughts, we make the world." - Buddha
IMHO, We don't need to save the World. It is enough if we save ourselves from ourselves. The need of the hour is not vain glorious interventions, but self-restraint and self-correction!
The Mind is the Final frontier.
Well, not to over-philosophise, "technological solutions" should not be considered as separate from the goal of "human dimensions"... the global scientific jargon has witnessed, over time intervals the last decades, the introduction of "terms" that have captured the attention of scientists (usually, introduced by some advanced country scientist or research center, then taken up by UN or WB or other international organisations people... & from there, those terms start spreading around to be used by the rest of the community for some time, untill another "term-break-through" comes along... & so on. One can easily find these terms out starting from the UN conference on environmental issues since the early 70's of last Century.Following
- How can we use matrix computations for state space modelling?
State space modelling is known to be good application of Linear Algebra. But, I couldn't find any clear idea on how we can use matrix computations in it. Can somebody help me to identify the way that matrix computations can be applied in state space modelling?Following
- Do you prefer minimally invasive or conventional open surgical procedures for radical cholecystectomy for gallbladder cancer?
Is it a must to perform open surgery?
Redical resection of the gall bladder for cancer necessitate resection of rim of liver tissue surrounding the bed of the gall bladder, in our center we used to do it through open laparotomy in both situations ( if diagnosed pre operatively or histologically after cholecystectomy) provided that the there are no mets or distant lymph nodes.Following
- Can be analysis both of phytol and alpha tocopherol by the same extraction and same GS-MS method?
I have silage grass sample, I consider that by the one extraction sample (sample will be extracted on Acetone 80% with 25%KOH), can I quantitative both of phytol and alpha tocopherol by GS-MS system?
Thank you very much Salvatore Chiavarini!Following
- Why core-shell structured Er doped NaYF4@SiO2 nanosphere still can recieve light and emit light?
As we know Er doped NaYF4 can be excited by near-infrared light and then emit visible light. But why after cover a nonporous silica layer, the material still can recieve light and emit light. The light can penetrate the silica layer? How?Following
- What is/are the reason(s) for using RNaseI in a CLIP experiment vs RNaseA/T1 Cocktail?
I am interested in understanding RNA-Protein Interactions and to get a list of RNA targets bound by the protein of interest, I am carrying out CLIP. I came across three different protocols:
a) HITS-CLIP (utilizes RNase A/T1 Cocktail)
b) iCLIP (RNase I)
c) PAR-CLIP (RNase T1)
I understand the differences in the three different protocols. However, I don't understand the rationale behind using the different RNases in these experiments. Someone please explain.
- Can anyone suggest a cheap method to purify proteins in 96 well plate without inactivating them?
I'm currently trying to analyse the activity of recombinant proteins but seems to get some kind of disturbance, either from the buffer (Bugbuster) that seems to interact with the substrate, or from the cell lysate. So I want to find a good cheap method for enzyme purification in 96 well plate.
The expression organism is E.coli and the recombinant proteins have a HIS-tag.
Please suggest a cheap method to purify recombinant proteins.Following
- Is there any reason why the rate of a reaction would decrease with substrate concentration, once it reaches saturation?
I am trying to determine the kinetic parameters of an enzyme with different substrates, from 0.1 mM to 5 mM. After a few increments (up to 1 mM), instead of the rate of reaction (measured as absorbance/min) stabilising and remaining constant, it starts to decrease. Is my enzyme being inhibited by the product? This is an esterase, and I have not heard of such a phenomenon in these enzymes. What else could be happening?
Yes, it is likely that several % isopropanol is inhibitory to the enzyme. If possible, either dissolve the substrate in the assay buffer, or at least keep the solvent concentration constant.Following
- Can interpretive structural modeling be applied to leadership attributes research?
I am a planning to carry out research in attributes of successful business leaders. i want to understand if it would be good idea to use ISM to develop model with hierarchy and relationship for success attributes.
The following article could be useful to your study:
Reza Sigari Tabrizi, Yeap Peik Foong, Nazli Ebrahimi "Using Interpretive Structural Modeling to Determine the Relationships among Knowledge Management Criteria inside Malaysian Organizations". International Journal of Social, Education, Economics and Management Engineering Vol:4, No:12, 2010.
It's free downloadable in internet.Following
- What makes it difficult for guidelines to be followed?
Benefits of restricted transfusion vs. liberal in certain patient groups; No role of renal dose dopamine; No role of FFP to increase serum albumin levels; Voluven (starch) predisposes to increased bleeding post-cardiac surgery, etc. Such and many others. Inspite of adequate proof, what are the factors that you think or may have encountered which make non-compliance with the published studies?
One also needs to keep in mind that guidelines are rarely universal as they try to be. They very seldom take into account the broader political, social and cultural implications, and that presents an obstacle in their implementation. So sometimes it is very hard to explain if such a deviation occurs. So there is a fine line when making and following guidelines.Following
- How can I make fluorescence embedded gel for mechanical force measurement?
I am trying to fabricate gel with uniformly distributed fluorescence beads
so that by measuring relative intensity of fluorescence signals, calculate
1. how much the gel is pushed
2. how much mechanical forces(compressive) are applied to the gel
I know there are many factors needed to be consider in order to derive compressive force from gel but first want to fabricate the gel and test out.
If there are any commercialized fluorescence gel with known young's number that would be perfect.
The technique is described by M Dembo you use PMMA and cross link coillagen to the surface. Dembo used a sphere sinking into the surface and we used an AFM. The method is well describedFollowing
- Hello everyone. I was in need of sector wise district level GDP data for India (for the state of Assam specificaly). Can anybody help?
A detailed sector wise (primary, secondary and tertiary sectors separately) data will be of much help.
i would suggest if you like to contact to Prof Mallikaqrjun , School of Management , Nirma University , Ahd , who has done pioneer work on district level data of GDP.
thx + wishesFollowing
- Is allergy a real issue in chitosan from shellfish origin?
I am having difficulties in finding scientific data on this topic.
Now I did!
Thank you very much for the kind help!
If the topic is of your interest, I found this other article also very relevant:
Mar. Drugs 2010, 8, 292-312; doi:10.3390/md8020292
Riccardo A. A. Muzzarelli
- Does anyone know about hot wire anemometers?
i have a hot wire anemometer DT-8880 that i use to assess ventilation performance in naturally ventilated hospital wards. my question is regarding the assigned area that is used to calculate the volumetric airflow. in case of more than one opening in the ward, shall i enter the area of the smallest opening or shall i sum all the opened windows area? or shall i take average?
Dear Alia Amer Hegazy,
this depends on the reason for the measurements. If you want the total volume flux (air-exchange-rate), usually every opening has to be be measured and calculated for itself. Afterwards the volume flux (or air-exchange-rate) can be summed up over all results. If the air velocity is the same for each opening (same speed AND same direction (outwards or inwards), you can summarize the area of the openings (Vflux =v*A).
- I search for an article or a text about non-dominated sorting genetic algorithm(NSGA). Can anyone help me?
i search about an article or a text about non-dominated sorting genetic algorithm(NSGA). if any person can help me?
you can find n number of recent publications in www.freefullpdf.comFollowing
- What types of tourism in cities best influence the urban poor?
Many types of tourism attempt to be helpful to the poor, volunteer tourism, slum tourism, and community tourism as examples. How do these really affect those dealing with urban poverty? Which model is better, or do we need a new model?
My student's study hasn't been published, but I can send you the file if you're interested in it.
You're right. Other stakeholders from outside shoud be incorporated, but they have to be logically more or less same-minded and have no verted financial interests, like tour operators or other large private tourism stakeholders could have.
I think you could define both of them separately; they are not at all the same even though there could be some shared issues or points.
Your case study seems interesting to me, i.e. Mexico City. I'm taking part at a reserach project which aimes to compare the conflicts which arise from UNESCO built heritage in Mexico City, Rome and Beijing.
- Can we consider that a multi-population genetic algorithm is the special case of parallel genetic algorithm?
Can we consider that a multi-population genetic algorithm is the special case of parallel genetic algorithm? Or we can not consider that at all.Following
- How do I measure the density of small quantities of material (glass)?
I need to measure the density of glasses, which unfortunately I got in very limited and small quantities: around 50 mg, both in powder form and in bulk. I have been trying so far: Archimedes's method for determining the density (in ethanol - water sensitive material - and in air), Guy-Lussac pycnometer (the smallest I could find - 5ml - encountered problems with this also because of the liquid medium: ethanol/isopropanol, due to rapid volatillization). I have access to helium pycnometer as well, but to my knowledge, I need at least 2 g of sample for accurate determination. If somebody encountered this problem likewise, I would like to hear about a solution. Thank you in advance.
Perhaps the simplest tool is to measure the volume of the piece of the bulk glass by a digital camera or microscope, and use a micrometer to get the thickness. Then weight it. If the shape is irregular, some software can be used to calculate the area.
Accuracy of better than 5% can be achieved, i would guess.Following
- Why isn’t nutrition a bigger part of conventional medical school education? Diet is arguably the single most important preventive measure for healthy aging because it affects the functioning of every organ in the body and is a factor both in the development of disease and in recovery.
I think vitamin activity is more important than any level of a specific vitamin. Vitamin C activity is the sum effect of dietary sources of natural L-ascorbic acid, numerous bioflavonoids (vitamin P) including rutin and around 4,000 other compounds, folates (which aid protein breakdown in combination with Vitamin C), tyrosinase (enhances white blood cell effectiveness), Factor J (assists the transport of oxygen by red blood cells), Factor K (clotting factor) as well as Cu, Zn and Fe to provide a short list.
Measuring or dosing with ascorbic acid alone is like examining a footprint and ignoring the condition of the animal that made it.Following
- Can anyone suggest the methodology for studying Climate change impacts on freshwater quality and biodiversity and its future status?
I am working on climate change impacts on freshwater systems and its biotic communities. I would like to get valuable information and suggestions from the researchers. If possible, suggest me a suitable methodologies for the above study. I have some ideas too.Following
- Which Real Time PCR machine is best suited for HRM analysis in Brazil?
I would rule out Lightcycler 480 and CFX96 from Roche and Bio-Rad because of their poor customer services. Are there other good options? If anyone has experience with Qiagen Rotor-Gene q here in Brazil i would like to hear that. Thank You, kind regards!
We have used for a number of years equipments from Life Technologies (now Termo Scientific). In our experience, they work very well.Following
- Is there any body doing PCR on pfrct,pfmdr, pfdhfr and pfdhps now and getting succesfull results?
I am presently doing PCR on on pfrct,pfmdr, pfdhfr and pfdhps using MR4 donated primers and positive controls: 3D7, Dd2, FCR3 and V1/S. The controls seem to be giving me expected band sizes but my test samples are misbehaving.
Can you be more specific. Are they not working or giving the wrong band sizes or too many band and do you have any additives eg dmso, betaine in your reaction mix . What is your cycling conditions ?Following
- Is there anyway to estimate temperature gradient in forest fire?
I would like to know if there is any way to estimate the temperature at some distance from a fire front (forest fire, wildfire). We want to know the vertical and horizontal temperature gradient which is generated by the front of a forest fire, to know how the tempearure is modified prior to vegetation burns.
We are interested in knowing how temperaute increases as a fire front approaches.
Thank you very much.
This is interested and Practical question in the field of fire in rangeland and forest, These factors are important: relative humidity, climate conditions and height Above sea level and Latitude. In addition, please study Hopkins equation about relationship between height Above sea level and Latitude change.
- Can anyone suggest a suitable protocol (UV-Vis Spectrophotometric) for Vitamin B complex (B1,B2,B3&B6 separately) estimation from rice grain?
I am in the process of estimation of nutritional value of some rice land races from Indica rice (Oryza Sativa L.) grain. I found HPLC method and Titrimetric methods for Vitamin B Complex analysis. But I want to know if there are any available protocols and methods for estimation of Vitamin B Complex (separately B1,B2,B3&B6).
I hope below files was useful for you
J Assoc Off Anal Chem. 1985 Jan-Feb;68(1):83-5.
J AOAC Int. 2008 Sep-Oct;91(5):1059-69.
J Assoc Off Anal Chem. 1983 Jan;66(1):158-60.Following
- Have you conducted empirical research about juvenile fire setting?
I am conducting an analysis of records of intervention with juvenile fire setters, searching for correlates between the identified risk factors (social, environmental, behavioural, psychological) in the young person, and the methodologies used to set fires - the versatility of the fire setting.
I have not found much research that has been conducted to date that links these artefacts explicitly.
Are you aware of research that explores the interconnection between risk factors and methodologies?
Perhaps you might also find these two articles useful for your research.DOI:10.1080/14330237.2011.10820511 and http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158524/
These are my publications as I have researched into conduct disorder issues (antisocial behaviour among adolescents aged 10-18).Following
- How does being bilingual affect a person's identity?
As language and culture are intertwined, I was wondering how a bilingual person develops his/her cultural identity. Does the person acquire the culture of L1, or that of L2? I'd appreciate your opinion.Following
- Magnesium chloride works more intracellularly than magnesium sulphate. What are the impacts on clinical effects?
Magnesiumchloride has more intra cellular effects while magnesiumsulphate has more extra cellular effects. This explains that magnesium sulphate is clinical less effective but why is it then also more toxic as the toxicity effects are primarily intracellular?
intravenous given magnesium reduces the opioid requirements per operative by reducing the sympathetic outflow.
Simple reasons of acidosis because different abilities of chloride and sulphate ions upon interations with cellular parts and phsiological pH changes drastcally....
Follow this.......Roche, Block, sonie and wilson.....Inoganic med chem bookFollowing