Science topics: Physical SciencesBiophysics
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Biophysics - Science topic
biophysics, protein folding and stability, spectroscopy, bioinformatics, molecular dynamics. . . .
Questions related to Biophysics
Press release, 22 October 2024
Understanding the physics of cancer, preventing metastases: Leopoldina honours the physician Bahriye Aktas and the biophysicists Jochen Guck and Josef Käs with the Greve Prize
Dealing with metastases is one of the major challenges of cancer therapy. More than 90 percent of deaths caused by cancer are linked to metastases. Understanding the conditions that cause cancer metastases and how these move through the body is key to developing new approaches to cancer treatment. Biophysics can provide valuable insights, as cancer is also subject to the laws of physics. In honour of their groundbreaking insights into the movement of tumour cells, the physician Professor Dr Bahriye Aktas, and the biophysicists Professor Dr Jochen Guck, and Professor Dr Josef Käs are receiving the 2024 Greve Prize from the German National Academy of Sciences Leopoldina. The award, endowed with 250,000 euros, is donated by the Helmut and Hannelore Greve Foundation for Science, Development and Culture.
The biophysicist Professor Dr Josef Käs from the University of Leipzig/Germany and Professor Dr Jochen Guck from the Max Planck Institute for the Physics of Light in Erlangen/Germany are leading global scientists in the physics of cancer. Their research, some of which they have conducted jointly, investigates the physical properties of cells when they interact with surrounding tissue. They have managed to demonstrate how tumour cells actively change from solid and stiff to a fluid and soft condition in order to move between the dense tissue of the human body and form metastases. This discovery has led to a paradigmatic shift in how cancer cells are viewed and motivated collaboration with the physician Professor Dr Bahriye Aktas from the University of Leipzig Medical Center. Aktas has made it possible to study human tumour samples directly after operating and thus also live-cell microscopy of the active deformation of cancer cells. Building on the work of their predecessor Professor Dr Michael Höckel, this raises the question of what limits cancer cells in the body experience. “Bahriye Aktas, Jochen Guck, and Josef Käs provide an impressive example of how interdisciplinary basic research can significantly deepen the understanding of cancerous diseases,” says Leopoldina President Professor (ETHZ) Dr Gerald Haug. “Studying the behaviour of tumour cells from the perspective of physics and linking it to direct insights gained from medical institutions has the potential to develop completely new means of treating cancer.”
The potential for cancer treatment is already apparent with respect to breast cancer. Whether the cancer has metastasised or not is key in determining the success of therapies. To date, however, it has not been possible to accurately predict when a tumour forms metastases. Käs and Aktas, working together with Professor Dr Axel Niendorf (Hamburg/Germany), managed to identify markers that, in combination with existing criteria, are significantly better at indicating a tumour’s potential to metastasise. They have done so using biophysical concepts, the central idea of which – that metastasising cancer cells must be softer – Jochen Guck played an important role in developing. Cancer cells in primary tumours are, at the local level, very solid and densely packed. In order to release themselves from the original tumour and move through the human body, cancer cells must soften, allowing the cancer cell aggregate to become fluid. In the study carried out by Käs and Aktas together with Axel Niendorf, the scientists identified the histological characteristics of the cancer cells that become fluid: they were longer and had deformed cell nuclei, allowing them to “squeeze” through neighbouring tissue. Their study of more than 1,000 breast cancer patients offers a strong indication that these deformed cell and nuclei forms can be used as a reliable marker for a cancer’s aggressiveness, and to predict a tumour’s potential to metastasise. This could permit breast cancer treatments to be more individually tailored to patients. In Erlangen, parallel to the activities in Leipzig, Guck developed a high-throughput method to measure the deformability of cells (real-time deformability cytometry, RT-DC). This method is particularly suited to finding substances that can change cancer cell mechanics to prevent metastases.
Bahriye Aktas (born in 1975) is Professor of Gynaecology at the University of Leipzig and Director of the Department of Gynaecology at the Leipzig Medical Center. Aktas studied medicine at the Justus Liebig University Gießen/Germany. She completed her medical training as a gynaecologist and obstetrician at the University Hospital Essen/Germany, obtained her habilitation there in 2013, and was appointed Associate Professor in 2017. That year she switched to the University of Leipzig. As a gynaecologist, her focus is on minimally invasive and robot-assisted surgery, which is used for gentler and precise operations with improved chances of healing, and she also has a particular interest in surgery for cancer treatment. She and her predecessor have helped to globally establish new operation methods that take into account how a tumour spreads.
I ran a 100ns molecular dynamics simulation of a protein-membrane system where the protein is 10 angstroms away from the membrane. After concatenating the trajectory files and performing post-processing (centering the protein-membrane complex), I noticed that the protein sometimes appears to go below the membrane for some frames in the visualization (Figure 2_462thframe) from the normal orientation (figure1_461thframe).
I'm unsure if this is an issue with the simulation itself or if I'm handling the periodic boundary conditions (PBC) incorrectly during post-processing. I've tried various gmx trjconv -pbc options, including -ur rect and -ur compact, but the problem persists.
Could someone please provide guidance on how to resolve this issue in GROMACS?
Dear colleagues,
I defended my Ph.D. thesis in October 2016 and now I am looking for a postdoctoral position in microscopy (AFM, TEM, SEM) and biophysics of microorganisms (especially, viruses, I like them :)).
My CV is attached. If there is an open position in your lab, please, write me.
Best regards,
Denis
I am trying to make a simplified model of the movement of meiofaunal animals in marine sediments.
Depending on their mode of movement, meiofauna can be classified as either "interstitial" (i.e. they move through sediment particles) or "burrowing" (i.e. they displace particles to move).
The organisms I am interested in, the kinorhynchs, move by anchoring an eversible introvert armoured with hook-like structures (scalids) in the sediment and actively pulling on them. That means that the locomotion of these animals mainly relies on the resistance offered by the sediment matrix in response to the force exerted by the scalids. Thus, it should be possible to make a study of momentum or quantity of movement with the weight of these organisms and the weight of the sediment through which they move. This could help us better understand how these animals move and how they are distributed according to the granulometry of the sediment.
However, this "model" becomes more complicated in fine sediments. It is relatively acceptable to assume that the resistance offered by coarse sediments, such as sand or gravel, is primarily due to the weight of the particles, and other minor forces exerting extra resistance can be neglected (for the purposes of this model). However, in fine sediments the resistance to displacement is (possibly) not exerted only by the weight of the particles, but is much greater than the sum of the weights of the grains due to other elements such as electrostatic forces between particles (and possibly others).
My questions are:
1. Are these assumptions correct?
2. Is there any way to calculate the resistance of fine sediments to the movement of these animals comparable to the resistance exerted by sandy sediments due to the weight of their particles?
Comments, suggestions or related literature are welcome.
Thank you very much,
Alberto.
Respectfully, which esoteric beliefs are the least plausibly true ? Why?
1)Scientific materialism because the fundamental choice to reason, DESPITE UNCERTAINTY, requires more than material. Source:
2)Reincarnation because if every entity is unique, or might as well be due to UNCERTAINTY, then sharing spirits is less likely. Source:
This question refers to biophysics.
I am searching for a dataset in ASD that contains EEG+ECG signals and biophysical data of the participants. The biophysical data can be in the form of either blood data (neutrophils, T-cells, lymphocytes, etc) or questionnaire (sleep problems, gut problems, allergy, autoimmunity etc). Any input is greatly appreciated.
Thanks.
Does anyone know an institute/research facility in Europe running research in the field of cancer therapy and willing to accept a student of Micro- and Nanotechnoligies in Biophysics for Erasmus+ holiday traineeship?
A NEW METHOD FOR ELECTROCHEMICAL ETCHING: I. Results with dc Voltage.
L. Tommasino, G. Zapparoli, F. Caiazzo
Thanks in advance.
I am reaching out to #researchers in the field of #Biochemistry, #Biophysics and #Bioinformatics, for collaborative partnership in scientific research. The researcher should be academic staff at the tertiary institutions in following listed countries:
#Afghanistan
#Angola
#Bangladesh
#Belarus
#Belize
#Benin
#Bhutan
#Burkina Faso
#Burma
#Burundi
#CaboVerde
#Cambodia
#Cameroon
#CentralAfricanRepublic
#Chad
#Comoros
#Congo
#CookIslands
#Cuba
#Democratic People's Republic of Korea
#Democratic Republic of the Congo
#Djibouti
#Dominica
#EquatorialGuinea
#Eritrea
#Eswatini
#Ethiopia
#Gambia
#Ghana
#Grenada
#Guinea
#Guinea-Bissau
#Guyana
#Haiti
#Iran
#IvoryCoast
#Kenya
#Kiribati
#Kyrgyzstan
#Lao People's Democratic Republic
#Lebanon
#Lesotho
#Liberia
#Madagascar
#Malawi
#Maldives
#Mali
#Marshall Islands
#Mauritania
#Micronesia (Federated States of)
#Mozambique
#Myanmar
#Nauru
#Nepal
#Nicaragua
#Niger
#Niue
#Palau
#PapuaNewGuinea
#Moldova (Republic of)
#Rwanda
#SaintHelena
#SaintLucia
#SaintVincent and the #Grenadines
#Samoa
#SaoTome and #Principe
#Senegal
#Sierra Leone
#SolomonIslands
#Somalia
#SouthSudan
#Sudan
#Suriname
#Syrian Arab Republic
#Tajikistan
#Timor-Leste
#Togo
#Tokelau
#Tonga
#Tuvalu
#Uganda
#Ukraine
#Tanzania (United Republic of)
#Vanuatu
#Yemen
#Zambia
#Zimbabwe
Interested researcher should kindly email to hezesapience@gmail.com with the subject: Research Collaboration from "your country".
Thanks.
Toluwase H. Fatoki
Visionary @ Heze-Sapience International, Nigeria.
Lecturer @ Department of Biochemistry, Federal University Oye-Ekiti, Nigeria.
Is there any system with small molecule binders and a short protein tag that is higher affinity than 6xHIS-NTA?
Have you noticed, formation and dissociation of triplex DNA is not fully reversible upon pH titration? After several cycles it becomes almost irreversible, i.e. fold in triplex conformation. Any thoughts?
On Wednesday, September 27th, we will have journal club (seminar) about dynamics and biophysics of non-canonical DNA. Please join for free :)
Hello everyone! We have organized a special topic "Emerging Tools, Concepts, and Applications in Multi-Scale Mechanobiology" on the journal Frontiers in Bioengineering and Biotechnology (IF=5.7, JCR 1), which is currently accepting submissions, and the deadline for submission of articles is 2024 January 23.
The topic covers but is not limited to:
• Cell/nuclear mechanobiology, Tissue biomechanics
• Engineered biomaterials / Matrix biology
• Bioinformatics-based approaches in mechanobiology
• Tumor microenvironment
• Cardiovascular physiology and pathology
• Stem cells and regenerative medicine
• Mechanobiology-based therapies
• Multi-scale modeling.
Contributions are welcome! It is also possible to send me the abstract at my email: zengxi@link.cuhk.edu.hk
For more information, please visit the dedicated website. Thanks for the support! Here is the website for the special topic: https://www.frontiersin.org/research-topics/58995/emerging-tools-concepts-and-applications-in-multi-scale-mechanobiology
I'm asking for experts who's interested in neuroscience, philosophy of mind, philosophy of religion, biophysics or artificial intelligence systems and computation or related fields. Thank you!
Looking for a sequence or vector map of pEC86, a plasmid which expresses E. coli cytochrome maturation (ccm) genes.
Here is a reference for the plasmid:
Arslan, Engin, et al. "Overproduction of theBradyrhizobium japonicum c-Type Cytochrome Subunits of thecbb3Oxidase inEscherichia coli." Biochemical and biophysical research communications 251.3 (1998): 744-747.
I searched yesterday and could not find any references, apart from hypercubes etc, to mathematical modeling using 4 dimensions other than my articles on arXiv and RG. That may explain why the role of 4/3 scaling has been unnoticed by physics.
I think a fourth dimension does play a role in modeling:
3/4 metabolic scaling.
Peto’s paradox
Brain weight scaling
4/3 fractal envelope of Brownian motion.
Clausius 1860 article on gas molecular mean path lengths.
Waterston on the energy to maintain a levitating elastic plane in a gravitational field (Roy Soc 1892 publication of 1845 submission).
Dark energy.
Are there any others?
Several articles on RG discuss 4/3 scaling, which involves the 4th dimension, including:
Preprint Dark energy modeled by scaling
Preprint Flow as a fourth dimension
and several other RG articles back to .
By genetically modifying we can alter some properties of plants. But can we modify the biophysical, optical or thermal properties of leaves?
The phrase in the Title line imitates Karl Popper’s All Life is Problem Solving.
Since thermodynamics plays a role in life processes, it was surprising that searching “All life is thermodynamics” on Google on August 16, 2022 gave no results.
Don’t organisms seek to optimize and preserve the entropy of their internal energy distribution? And to optimize their use of energy and outcomes based on energy inputs? Aren’t survival and procreation ways of preserving previous products of energy use?
Is there justification for the statement, All life is thermodynamics? Or is the statement too simple to convey any insight?
Schrodinger in What is Life referred to thermodynamics, statistical mechanics; chapter 6 is Order, Disorder and Entropy. And more recently there is: J. Chem. Phys. 139, 121923 (2013); doi: 10.1063/1.4818538 Statistical physics of self-replication by Jeremy England.
Hey everyone..
Would like to get your views on certain questions relating to Blood Pressure & cardiovascular physiology...
How is vascular pressure generated in the body? Is it because of the heart or the vessels?
What happens to pulse pressure when central artery stiffness rises?
Hello
I need it urgently
Can you give me articles in the field of aflatoxin that are both biophysical and bioinformatics?(for example biosensor)
Which textbook do you recommend for an introductory biophysics course (aimed at 2nd year students from different disciplines: https://apps.ualberta.ca/catalogue/archive/course/bioph/201/1810)?
Is it possible to suggest a title (Biophysics of food) that includes all three NMR SAXS DSC devices?
Biophysical assay involves cleaving a quenched fluoregenic substrate that results in increased fluorescence. Difference between racemic mixture and pure components came to be ten times different in terms of IC50!
I have to create .cgc file for vitamin E in VMD. Kindly help me to create it. I need literature for it. Thanks in advance
Hello,
For intramolecular FRET, I've always had one position labeled with the donor and another position with the acceptor, in a controlled way (e.g. one at a lysine and one at a cysteine). But I need to figure out if I can do FRET if the two positions are the same reactive group (in this case, both positions are cysteines).
The proposition is that the purified protein's 2 positions be labeled with donor and acceptor randomly, so that the two positions can be donor-acceptor, donorx2, acceptorx2, donor-unlabeled, acceptor-unlabeled, and unlabeledx2 in a mixture.
I am worried that the background from the improperly labeled proteins in the mixture will obscure the signal from the properly labeled protein to such an extent that the FRET has too small a dynamic range.
Is it better to have even donor:acceptor ratio or should one or the other be in excess? Should the labeling be saturated or substoichiometric? Not sure what will work best.
Has anyone tried something like this? Did it work? What helped?
Thanks!
~Beverley
Hello. I am working on a kinase that binds to ATP. I cocrystallized the protein with the ATP analog AMP and solved the structure. However, while performing ITC, I am not getting a complete saturation. The attached image is for a reaction wherein a 1:10 ratio of protein and the ligand (AMP) was used. Later I also increased and decreased the ligand ratios, but there was no binding. I have also tried using different protein concentrations and repeated the experiment multiple times, but the results remain the same.
Also, the N value for one site binding is 0.01.
So, what could be the most probable reason for such a result?
I was saddened to receive a message today that Dr Jean Garnier, a dear friend, mentor, and scientific colleague, has passed way. He held the Order of Honors in Agronomy (Mérite Agricole), Officer, Order of Honors in Education (Palmes Académiques), Knight. He has also held a laureate position at the Ministry of Agriculture, USA, and the position of Research Director at the French National Institute for Agricultural Research. He was until quite recently the Editor in Chief of Biophysical Reviews, a journal sponsored by the International Union of Pure and Applied Biophysics of which he has been President. He was a widely respected expert in protein science and a founder of bioinformatics. He wrote many scientific papers, and he was a huge influence on my work and the work of many others. We coauthored a textbook on proteins and protein engineering that was widely used in universities. Under his guidance, our research and early papers together, particularly on the prediction of protein secondary structure and protein modeling, achieved many thousands of citations. The GOR method is still widely used today, and I saw that it played a significant role in the published research of many protein scientists responding to the rise of COVID-19. We kept in touch, and he will be very much missed.
I have noticed while reading different publications that some have used collagen to coat slide/chamber surface in fluid-flow cell experiments, while others used fibronectin. Does coating rely on the type of cells that I am going to use? Example: collagen coating for bone cells, fibronectin coating for endothelial cells?
It requires about 5.3 kcal/mol (or 8 kBT) of energy to break one phoshodiester bond of DNA. How do these enzymes cut the DNA only by using thermal energy and not ATP? I am only considering the ATP-independent restriction enzymes (Type II). How do these enzymes manage to generate the necessary energy? I couldn't find the exact mechanism with energetics of restriction enzymes cleaving DNA. Please provide me any relevant references.
During AFM imaging, the tip does the raster scanning in xy-axes and deflects in z-axis due to the topographical changes on the surface being imaged. The height adjustments made by the piezo at every point on the surface during the scanning is recorded to reconstruct a 3D topographical image. How does the laser beam remain on the tip while the tip moves all over the surface? Isn't the optics static inside the scanner that is responsible for directing the laser beam onto the cantilever or does it move in sync with the tip? How is it that only the z-signal is affected due to the topography but the xy-signal of the QPD not affected by the movement of the tip?
or in other words, why is the QPD signal affected only due to the bending and twisting of the cantilever and not due to its translation?
It need metal ion as cofactor. How does the charge balance affect docking result?
What are the Biophysical and Biochemical techniques that used in Recombinat DNA technology??
One might argue: Animals increase their survivability by increasing the degrees of freedom available to them in interacting with their environment and other members of their species.
Right, wrong, or in between? Your views?
Are there articles discussing this?
I am computing Van der Waal interactions in python for a peptide of size 10 residues for various conformations. The total conformations (or the number of PDB files is 300,000). Is it possible to compute only the 1-4 atom distances to compute Van der Waals interactions as the bonded and 1-3 atom distances are irrelevant when it comes to Van der Waal interactions using some python module?
Does the DNA remain stable or degrade at this temperature? Would there be any difference in thermal stability between supercoiled and linear forms of say, 3 kb plasmid.
Hello,
I intend to perform thermal unfolding of my proteins by CD, to determine their melting temperatures.
I initially scanned the proteins over a wavelength range of 250 -190 nm at 25 °C (in 20 mM Phosphate bufffer pH 7.4) to determine their structural content. The results confirm that the proteins are made up of alpha-helices (which is what i expected), with two negative bands at ~208 nm and ~221 nm, and one positive band at ~ 192 nm . See attached image!
Next, I will like to thermally unfold the proteins at a specific wavelength. Given the results attached, could anyone please suggest what wavelength would be idle to monitor the thermal denaturation of the proteins and why?
Best
Compiled allometric data might help to detect scaling patterns.
Or similarities in the scaling relationships might suggest connections otherwise too subtle to find.
Does such a list exist?
Does such a list exist for biological phenomena?
If such lists do not exist should they?
I want to know if the number of fringes and their shape is an important factor for the accuracy of phase definition?
Hello,
Our old but not to old DynaPro Plate reader I does not work anymore and Wyatt does not want to investigate the problem as the instrument is 10 years old. We have the money to pay them but they really do not want to loose time on it...
We would like to know if some of you know DLS instruments that are compatible with the measurement of several conditions (at least 30 conditions) in parallel. Of course the goal is to find a company that is able to do a maintenance.
Best,
Sébastien
If I use AVI, BSI, SI and TI as biophysical factor.
Hi I have attached the link to article and the table from the article with this question, I wanted to know how the value of 0.7 s-1 is calculated from the slope and intercept values using the bell evans equation. The values of slope is 85.3 and intercept is -351.
Thank you in advance
I have a set of Ramachandran angles. I wish to make Ramachandran plot out of it with standard allowed region contours in the background in Python. I couldn't do that in python. If not in python, Is there in anyother software where I can do this?
The question was prompted by articles like this: https://theconversation.com/an-ancient-retrovirus-has-been-found-in-human-dna-and-it-might-still-be-active-56844
Is anyone aware of a scientific answer, specifically what type of biochemical or biophysical triggers can trigger activation?
Thanks.
Biophysical remote sensing pertains to the detection and analysis of the biological and/or physical characteristics of a landscape, particularly its vegetation and soil.
In carrying out a research in biophysical remote sensing and it's application to climate and land change science what methods or approaches can be used?
This question leads me to ask another one.
Why do the osmoles of urea when they pass into the cell exert an osmotic effect and draw water into the cell, while when they were outside they had no effect?
Hi! I am quite curious about mitochondrial mechanobiology. How does mechanotransduction (both cell-matrix and cell-cell) affect mitochondial behaviour (mitophagy, mitochondriokinesis & ?) What is the signalling pathway behind (both transcriptomic/proteomic and metabonomic)? How are mitochondrial behaviours and signalling in wound-healing process? Are there some most nonnegligible/core article in this topic?
Thank you!
Hi,
I and working on a project for extraterrestrial life, and i need few work on the titled topic. If is there any data, recommend it or please discuss the evaluation mechanism.
Thank you,
Muhammad Furqan Ali
Hi everyone
Could you share your research and/ or other researches related to the application of magnetic fields in biophysics and Medical physics?
Thanks
I need a way to rotate my entire system (DNA and solvent) such that the axis of the DNA lies along the x-axis, but I want the periodic boundaries to be preserved. I added pictures of my system before and after rotation.
How can I edit things in such a way that the entire system is rotated, but molecules stay within the box? (basically the water molecules that were rotated down and went outside the box should reappear up inside the box)
Thank you in advance!
Dear Sirs,
I did not find this material on the internet. There are only mechanical models of some aspects of self-replication. Full mechanical model is absent. Of course it is enourmous problem if one precisely build it. But maybe there are simple and simultaneously more complete mechanical models? I prefer purely mechanical self-replicating machine but self-replicating robots are also good.
How can/should we distinguish between a Biochemical and a Chemical Reaction.
As per one explanation:-
Chemical reactions are discrete reactions with catalyst involved in the process where as in biochemical reactions there are a series of reactions involved with the product of one acting as the substrate for another and this complex process of interchanges taking place with the involvement of enzymes.
For a more specific example if we are conducting photosynthesis in vitro then it will be considered as a biochemical reaction rather than a chemical reaction.
But the dilemma stems from the fact that, even chemical reactions go through complex series of steps, like any organic synthesis reaction. In this case also there is the involvement of catalysts like enzymes. Thus, can we consider it as a biochemical reaction! But mostly we only attribute it to be a chemical reaction which is indeed the case.
So, what is the proper difference or point of distinction between a biochemical and a chemical reaction. How can we exactly relate that one reaction is a biochemical and the other is chemical!
I need brief information about the field of the researchers who work with bioimaging techniques in their researches. In Finland, there is the public concept that they think a researcher with biomolecular and biochemical background must stay in his/her old methods of researches which is work in the lab and pipetting, etc. I am so much interested to know is it true about all scientific groups that you cant get a chance of trying new techniques and also learning which suppose to be the main purpose of science and its progress or as I understood it is just an excuse? Science cant grows with a limit or making exclusiveness.
For the simulation purpose, I need force-field for Mn3O4. I searched and tried a lot but almost unable to get appropriate force-field parameters for it. Can anyone help me by suggesting or availing it ?
What impacts do these drivers have on socioeconomic and biophysical activities in the country
Dear all,
Besides biophysical or Biochemical approach, is there any other way of studying protein-protein interaction. I am planning to work on viral protein interaction with host proteins. The conventional method to study is yeast hybrid tool. However, I would like to explore other approach. Please suggest the way other that yeast as it takes huge amount of time and mutations issues are always a concern in yeast that results into some unexpected unexplained results. looking forward to hear from you.
Thank you in advance
Prem
What are the differences between Medical and Biophysics?
I'm taking some measurements using Raman spectroscopy of healthy pig eye samples using a new excitation wavelength and my supervisor said to choose a sample size to allow for spec/sens of 85%. These measurements will be identical just on different, healthy eye tissue to simply show that I obtain similar things each time. Is there a way to estimate/calculate what my sample size should be for this or do I need previous data, numerical limits etc? Any help would be great, thanks!
I have had unheard of success with protein crystallography lately from a super successful protein expression and purification batch.
I have attained a lately reproducible vast amount of crystals of no average size. Is there a way to tell based on appearance which of these crystals should diffract the best?
All these crystals grow from a clear droplet in 12 hours.
What's the most important parameter?
* transparency?
* size?
* how intensely it reflects light? birefringence?
* geometry?
It is well known that heating can denature proteins. However, what does happen to proteins in the case of short and ultrashort (microsecond or nanosecond scale) heating to extreme temperatures (100-1000 degrees of Celsius) ? Such heating occurs for example when applying ultra/short laser pulses or pulsed intense electric fields.
Solving the protein structure prediction problem by AlphaFold2(AF2) from sequence seems at its core a game-changing breakthrough. Major areas of biology and biophysics will thrive and others may become diminished or even obsolete.
Will AF2 hurt or benefit experimental methods for determination of protein structure? Structures of large macromolecular machines should be enabled by having accurate computational structures for subunits and components. X-ray structure value may become more specialized.
One thing that seems likely is that the already great value of sequence data (which is doubling every 8 months) is likely to become far greater by being more directly connected to spatial information. At its core solving the protein folding problem will enhance sequence impact and thereby increase the overall the pace of biology and biophysical advances by improving the ability of structural biology to better harness the flood of sequence data. How much will medical areas such as cancer biology and cancer drug discovery benefit? How about research areas such as protein design? What areas are likely to be most powerfully advanced and which most negatively impacted?
What do you think?
How should senior and early stage researchers position themselves to ride the wave of growing positive impacts and reduce research wipeouts when this new mega-wave adds constructively or destructively with current research waves of systems biology and single molecule and single cell advances? What should we change in training for graduate students and fellows to insure they are correctly positioned for science with reliable protein structure prediction?
AF2 may most strongly impact experimental determination of protein structure by multiple methods with possible benefits and negative impacts over time.
Some areas may need to quickly pivot or become obsolescent, whereas other may thrive.
Structures of large macromolecular machines should be enabled by having accurate computational structures for subunits and components.
The already great value of sequence data (which is doubling every 8 months) is likely to become far greater by being more directly connected to spatial information.
Overall the pace of biology and biophysical advances can be expected in increase by the ability to better harness the flood of sequence data.
What do you think?
Hey scientists,
I am intending to observe the extension of a short 10-mer primer on a 16-mer template. I just use a certain DNA polymerase to extend the primer on a templating strand with a matching or mismatching deoxynucleotide triphosphate (dNTP) and the necessary cofactor magnesium.
I was thinking that depending upon the polymerization efficiency, I might have products that are size "n", "n + 1", "n + 2", "n + 3", " n + 4", "n + 5", "n + 6" in size where size "n" is the size of dsDNA duplex without addition of dNTPs, or in other words no extension.
I was envisioning I just combine in a test tube the enzyme with the template:primer construct + the dNTPs of interest + MgCl2 and let the reaction happen for 30 minutes. Then I would denature my protein with heating the test tube to 50°C. (My polymerase isn't one of those thermal stable polymerases), and slow cool the test tube to room temperature.
I could run the products on an ethidium bromide stained gel with a control being a lane with just the template:primer construct with no extension, and then lanes with attempted extension of the dsDNA construct. If at least one base is added I want there to be a notable shift.
What resolution gel could achieve that?
4% Agarose or 16% polyacrylamide or something?
It would be cool, but it's not a big deal for me to distinguish exactly how many bases were extended from "n". So long as I can see an extension from "n" and I would be satisfied.
Thanks!
There is a growing interest in developing means of early detection of crop nutrient deficiencies. It has held that by the time a deficiency shows up in a soil sample, the crop is already under stress. Does crop sap analysis help to resolve this information gap? If so, how can we expand the use of this from high margin specialty crops to commodity crops?
So I am trying to crystallize a Protein:DNA complex with DNA at at least 5 times excess at basic pH with a certain poleythene glycol molecular weight (PEG) and a mixture of soluble salts at low concentration less than 110 mM. I was getting a microcrystalline shower at a certain concentration of the components but lots of amorphous brown precipitate.
So I tried glycerol concentrations logically from 0 to 5%. I blocked the microcrystalline shower at glycerol concentrations greater than 1%. I kept increasing the concentration of glycerol regardless and at glycerol concentrations higher than 5% (v/v) and all other components in the system no brown amorphous precipitate appears; total protein is soluble. At glycerol concentrations greater than or equal to 15% (v/v) all other components in the system, the brown amorphous precipitate comes back. When glycerol is @ 13% (v/v) I got some small crystals not a showers worth. But nucleation seemed to fall asleep and that was it.
Then I lowered the concentration of one of the salts potassium citrate monohydrate to 100 mM and I get a reproducible white haze or white sheen appear over the droplet from the edge. The haze now seems to appear at any concentration of PEG much less than or equal to the concentration of PEG that I would expect to give me crystals. I also think the haze is growing.
I have seen this haze before when I crystallized the free protein under totally different conditions with different components in the system and acidic pH. This white haze would move from the edge of the droplet towards the center and then medium sized to large crystals would appear out of the haze in less than 30 minutes. Those crystals diffracted and a protein structure was solved. Of course under these conditions, crystals haven't grown out of the haze yet. Crystallizing the more conformationally inflexible tight binding DNA complex is more difficult than it logically should be.
Is there a term for this white haze or any information I can read about it?
What does it suggest to you?
Thanks!
What happens when we culture cancer epithelial cells in TCPS?. Is the cell present as epithelial or differentiate into mesenchymal cells?.
Hello fellow scientists,
I have some additional questions about the dissociation constant for a protein binding ligand.
My main questions is if the protein concentration is much greater than the KD and the ligand concentration is still in excess of the K_D how much protein is bound?
For a Protein binding a ligand, we have the relationship:
P + L ⇌ PL . This has forward and reverse rates of binding, and ...
KD = {[P] * [L]} / [PL],
The fraction of protein bound (FPL) will be:
FPL = [PL] / ([P] + [PL]) = {[L] / ([L] + KD)}
If the ligand concentration is some multiple integer n of the KD we get this cool relationship:
[L] = n * KD ; n = 1, 2, 3, ... etc.
FPL= (n * KD) / (n*KD + KD)
= n / (n + 1)
What they teach you in school is that if the ligand concentration is at the KD, n = 1 then half the protein is bound: 1 / (1 + 1) = 1 / 2. This relationship also tells you that if [L] = 9 * KD then 90% of the protein is bound.
One can plot this relationship as I have.
So I have some questions assuming a reasonable good ligand interaction with KD = 10 µM,
(A) If [L] = 9 * KD, and fixed protein concentration = KD = 10 µM, how much protein is bound?
I think that 90% of the protein is bound.
B) Say you are a structural biologist and you need more ligand and protein than the KD at 10 µM,
If [L] = 500 µM (that is 50KD) and initial protein concentration is 100 µM (that is 10KD), then how much protein is bound?
Given the relationship I derived, {50 / (50 + 1)} = 98% of the protein should be bound.
But the protein concentration is beyond the KD so can that even be correct?