Hello all,

I'm in the midst of a transitional period, and looking to upskill in one or more ways. One of the things I'd like to do is gain some skills in computational protein-ligand modeling. I'm a metabolic and enzyme biochemist -- and I've done quite a bit of the "wet" cellular and enzyme assays with natural and synthetic effectors; however, I'm at a complete loss when it comes to modeling any protein/enzyme-effector interactions.

I did some marginal modeling in an introductory biochemistry course, but not in about 20 years, since I was an undergraduate. I believe I used RasMol at the time.

I'd like to be able to take a protein structure, and the structure of a small molecule, and "dock" the small molecule within the protein's structure in a visually appealing and informative manner. Possibly also some very rudimentary energy calculations; I'm not a structural biologist or a biophysical chemist, but it would be nice to know how favourable or unfavourable (i.e. how realistic) the docking would be, and where a small molecule would be most likely to bind to a given protein.

If possible, I'd love to learn in a sort of course or tutorial format, starting from the bare essentials and working my way up. Happy to pay for something reasonably-priced, or something free if available and reliable.

Thanks in advance for any recommendations!

My undergrad has a 3+1 system, with the 4th year being a thesis project. I want to do structural biology/mechanical biology. Here's the exp I've had:

• Industry internship (3 months), can get a good LOR
• 1+ year data analysis type of project (related to cancer), will be submitting for publication soon, can get LOR from this prof too, first author-level contribution to the project
• Fourth year project in structural virology (like a master's thesis) with coursework ( I plan to take graduate-level courses and a few math courses)
• Might do another odd project (chemical biology) with another prof
• Won first prize for poster presentation at a UG level science fest at my uni, no wet lab work but it was like a lit review and I proposed my own hypothesis (kind of like a research proposal)
• Participated and successfully completed a Stanford Bio course while at my uni this past sem, worked on a project to develop a low-cost diagnostic that I may take forward in the future
• A lot of science-related volunteering and EC work (at least 2-2.5 years worth)
• Resident Assistant for a year
• cgpa for 3rd year: 3.87, 3.93 for major in chem + minor in biology, got latin honours
• aiming for 3.9+ cgpa in the fourth year

Is there anything I can do to strengthen my profile?

I went to uni during covid and only achieved a 2.9 GPA due to severe depression spanning 2.5 years. (degree in biochemistry and molecular biophysics)

i’ve been working in an academic lab for the last year, and while i’ve gained loads of relevant skills, I don’t have any publications yet.

i want to pursue a phd in biochemistry, but I’m worried no schools will take me because of my college GPA and lack of papers.

so my question is … what exactly is necessary to get into a phd in biochemistry?

Does chlorophyll an emission spectrum always peak ~670nm for all plants? If it always about the same, does the emission spectrum vary a little like peaks a ~670nm +/- 20nm

I'm 22 and looking to finish a bachelor's degree within 2 years. I could finish a degree in biochem without any debt, BUT my college isn't a research Obviously everyone here is interesting I'm biochemistry so there is some bias, but is a degree on biochem worth it? Can you find good work within a reasonable time? Is there any work in Michigan for the field? From my understanding you really have to get a higher education to get into a job that pays a living wage specific to the career.

I could finish a degree in something like business within 2 years as well. It just doesn't feel impactful or difficult. I want a degree where I can get specialized knowledge.

Have you read a cool paper recently that you want to discuss?

Do you have a paper that's been in your in your "to read" pile that you think other people might be interested in?

Have you recently published something you want to brag on?

Share them here and get the discussion started!

I know the basics like intracellular, cAMP, cGMP, IP3, etc.

How do I remember where exactly the receptors are in the cell? Like I know estrogen receptors are inside a cell but I want to be able to deduce if it's on the nuclear membrane, within cytoplasm, or within nucleus.

Is there a general rule of thumb I can follow?

Could someone help me understand how if you used Dodecanol instead of Sodium dodecylsulfate in PAGE, the difference in how the two would behave and if it would leads to reliable molecular weight estimates?

I’ve searched high and low and read everything I have available but only became more confused.

Hi it's my first time doing rt-qPCR, and us having great difficulties in tracking the wells.

I have master mixes with all components (15 wells in total for each master mix), except the RNA (which I will add 1ul per well after loading 9ul of the mix).

I can't accurately keep track on the wells I loaded the liquids (the 1 ul RNA is even worse) since I can't see the reflections of the liquids in such a white plate at all.

Any tips? Thanks!

Hey everyone,

I was having a look into the physics behind how and why molecules move across the membrane and now I'm at a bit of a loss. I've read that passive diffusion is a product of entropy and the movement towards equilibrium across a membrane is just a matter of statistics when considering random movement (so there's no driving force behind the distribution in this case, but rather just the most likely statistical outcome of free moving molecules in a given area). However, if this is the case, why would you need an energy input to move glucose against it's concentration gradient if there isn't any "force" that the system has to work against? So is passive diffusion as a product of entropy and passive diffusion due to a concentration gradient different in nature? I get the reason why working against an electrochemical gradient would require an input of energy, but I'm not sure why glucose would ever need to be actively transported into the cell..

Any advice on this matter would be really appreciated!

I have been accepted into FSU Jena for Bsc. Biochemistry/Molecularbiology and and am still waiting for answers from Tübingen and some other Unis.

I am first doing a social year in Germany at a Institute for clinical brain research working in a lab so I have some time to decide but I am allowed to defer one application. But how do I choose which one? The modules are all similar, the only real difference probably being the "wildcard" modules. Any tips? I would like to specialize in Immunology/Epidemiology or oncology but I am not sure I can specialized in my bachelor.

Thanks in advance for any tips!

Hi, I am starting a biochem/biophysics PhD program in the fall and wanted to start some self study before the semester started. I come from a physics background and have basic chemistry knowledge as well. Does anyone have recommendations for introductory biochemistry texts that would be good with my background?

But I have tough time right know looking for an answer

Does beta turn found in beta sheet? Because it look exactly like side of bate sheet

I’m uncertain where to post this, but I think this subreddit might be best. To explain the title and the phenomenon I’ve observed I want to give some background. I graduated in 2020 from a structural biology lab. With some initial guidance from my PI, I did nearly everything on my own. By this I mean the molecular biology leading to protein expression, purification, assays, crystallography, data processing, and model building. Included in there would of course be lab maintenance (ordering, taking care of instruments, software management, buffer and materials prep).

My expectation is that anyone graduating from a biochemistry program could do these basic tasks. Not everyone would know crystallography obviously, but if one did a technique, they could explain the basic principles of the method (i.e. what is SPR and what does it measure) or how and why they purified a protein a certain way. Certainly not extremely detailed knowledge (like how do wigglers work or explain Geman-McClure restraints) but enough to understand the work done.

I’ve interviewed several postdocs lately and I’m surprised that my experience is not universal. I think 1/5 postdocs would fit the description of what I did (or easily surpass it), whereas 4/5 would not. It seems that the majority of them did one aspect of the work, as though they were in an assembly line. Some were “protein factories” who just expressed and purified proteins to hand off to the next person. Or they only did one set of functional assays (BLI, ITC) without understanding how their protein(s) were made or even the structural context that led to their work.

Two candidates stand out. One from a structural lab never built, refined, collected, or processed the data leading to their models. Rather their PI/senior postdoc did all the work and they only expressed protein. Another candidate from a well-known institution just took products from one core and fed it into another core, almost as a manager. This person was about to graduate with a PhD and was incapable of giving anything but a superficial overview of the techniques and aspects of their research.

My experience is limited to my locale, but is this normal? My mentors definitely did more than what I did, and I’ve encountered postdocs at my institution who have done and mastered much more than what I’ve done or will ever do. At conferences I’ve met other groups and this does not seem to be normal. Has anyone else encountered this phenomenon or is my experience unique?

What internship or entry level job can I get in the biochemistry field before I start my freshman year and throughout college?

Im after doing 1 year of biological and chemical science and then we had to pick an option, and based off grades you get your first or second choice. I wanted bioscience but got industrial biochemistry. Should i try to transfer if theres space thru the year or is an industrial biochemistry degree worth it? I want a job that doesnt focus on food but medicine instead, but most of the graduates say they got jobs with food processing.

I graduated this year with a 3.1 GPA and have no research experience (I tried hard to get experience but the profs always asked for my GPA and then Ghosted me). I've applied to lots of jobs and got rejected many times, I'm tired. I don't know what to do, I can't go back to school because I can't afford it. Does anyone have some advice for me?

Hi guys! I'm conducting my PhD in Biomedicine and I'm a bit stuck with the latest experiment we're running. I have generated a cell line stably expressing SRD5A1 and I have been able to detect its expression through Western Blot. Now I should assay its functionality. To do so, we want to treat the cells with testosterone and measure its levels (they should decrease as a consequence of SRD5A1 activity) using an ELISA kit and comparing the results to control cells not expressing SRD5A1 (whose levels should remain stable).

Here is where doubts arise. How much testosterone should I add to my cells? I have agreed with my boss to use 5 concentrations, and the ELISA kit standard curve goes from 3.9 pg/mL to 500 pg/mL. I have considered using 10, 50, 100, 250 and 500 pg/mL, but I'm not sure if they might be too low. Another approach I have considered is that I could use higher concentrations and then dilute the samples for the ELISA assay.

I don't want to mess it up with this assay as the kit is quite expensive. I would greatly appreciate your help. Thanks everyone! :)

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

Please point out if I made any errors in the paragrath below, have I made any factual mistakes ?

This info is mostly taken from what other people on reddit commented

AlphaFold 2 is not the only AI system working on protein folding and that AlphaFold 3 already exists.

There is sequence - structure. Given this string of amino acids, roughly how will it fold up based on all the other structures we've seen. Huge caveat... that training data is biased to well studied proteins and those that are most amendable to making crystal structures. Then there is structure -> function. What does this protein actually do? What reactions does it catalyze? How does it interact with other proteins?

The real goal here is sequence - function.

It's a misnomer to say it solves the folding problem because it doesn't take folding events into account. It predicts the end structure of a protein that has already folded, it is useful for structural predictions from sequences. It doesn't actually tell us much, if anything, about the folding pathways that a polypeptide takes to get to the folded state. With that being said, AF is really good at predicting structures of independently folding domains from sequence alone, better than any other tool has previously. Even when it hasn't seen structural templates of your protein before, it still does an incredible job.

AF is really good for generating hypotheses and allowing us to better choose where to focus resources in research. The predicted structure can give hints about associated function and also enables us to find out what is known about similar structures. Instead of stumbling in the dark, it can give us a head start, with a high degree of confidence. It isn't always correct, very long multi-domain proteins are scrunched up when in reality they're elongated, multi-protein complexes aren't predicted with as high confidence, and it isn't able to incorporate many non-proteinaceous cofactors (a handful can now be incorporated such as ATP), among other criticisms.

AF2 is good with proteins that are similar to ones that it has seen in the training data. It is decent with soluble monomer (single subunit) proteins (better than other methods). And even with soluble monomers, it's decent in getting the overall shape right, but there's usually some regions that are predicted pretty badly

Hey everyone! We are currently in the process of developing a running buffer recipe for a lateral flow assay. We have tired different combinations of casein, sodium azide, and tween 20. We’ve used both DI water and PBS for the base. We’ve adjusted the pH concentration, how long it sat in the refrigerator, different orders of construction, etc. We still can’t figure out how to make a successful running buffer and would love to hear some advice from you all, thank you!!

I live in the united states and have been a part of a biotech course in high school where i learned basic laboratory techniques, bioethics, and created some experiments of my own, analyzing data and writing papers.

What is day in life of the average biochemist degree graduate is like? What do you do on day to day basis? What would you recommend for someone pursuing that degree? And what is the salary like?

I am wondering what people's thoughts on NMR CSP are for a new form of enzyme engineering in industry. Enzyme engineering is something I would be interested to pursue as a career, and I enjoy the chemistry behind NMR. I am wondering if this is something you use often in your field or your thoughts on how it could be useful in your field.

Below is a quick summary if you've not heard of the technique before:

(I edited this to better describe the method as my previous attempt was poor. Thanks for the understanding, and hopefully, you still find this Interesting!)

A protein is selected, and it is tested using NMR in two states. It is first tested in an unbound form, then again in a ligand bound form. Both structures are crystallized to ensure they are in the correct conformation when tested. Using an H1 and N15 HSQC NMR plot, the difference in CSP between each amino acid pair is plotted. Using this, Z-scores are then calculated, and any amino acid with a score of 1 or greater is deemed significant. Only these "signifigant" amino acid positions are tested for because they were found to contribute the most to the proteins change in shape/binding to the ligand.Because of this, very few amino acid positions need to be tested. These "signifigant" positions are tested for with every possible amino acid mutation. In the studies i've looked through, it's been consistent that a.a with a Z-score of 1 or greater had significant results when mutated. Some studies even found that they only needed 3 amino acid mutations to create a Kemp eliminase from 3 mutations. It was also found that only another 3 mutations were needed to increase the function of the most efficient Kemp eliminas, at the time of the study, by 4-fold.

working on a research project and im trying to figure out how to construct a certain liposomal formulation. my goal is to construct a fluorescent labeled liposome that can target and enter the intracellular fluid of cholinergic neurons in the nematode C. Elegans.

My plan so far:
Liposomes prepared by forming a lipid film using egg phosphatidylcholine, cholesterol, and DSPE-PEG2000-Biotin, incorporating DiI fluorescent dye. Streptavidin is then added to bind to biotinylated lipids on the liposome surface, followed by purification to remove unbound streptavidin. Biotinylated acetylcholine analogs are conjugated to streptavidin-coated liposomes, purified again, and characterized for size and dye content using dynamic light scattering and fluorescence spectroscopy. Then do an in vivo test to assess binding specificity to cholinergic neurons in C. elegans, observed through fluorescent microscopy to track liposome localization.

Please any feedback would be appreciated. I'm in high school so I'm not a professional but im trying my best and any help would be appreciated. i want to create a research proposal so that i can conduct this experiment in an actual lab with a mentoring prof hopefully.

I recently got a scholarship to do Master's in germany. I have a few universities I have applied for but I am not fully decided on where to go. I am most interested in biophysical chemistry, that is things like mass spectrometry, NMR, structural biology, computational techniques etc. I want to do a masters to improve my knowledge and skills, especially in physics.

I currently have on my list of choices:

• TU dresden physics of life: from my understanding dresden is very strong in biophysics, but I am not sure how much structural biology/chemistry there is
• LMU biochemistry: Only issue here is they require an in-person exam (I live in Australia which is a long travel to do an exam)
• Konstanz life science
• Jena FSU biochem

I was also considering Max Planck's institutes Matter to Life program but I unfortunately missed the application deadline.

Finally, I am not too sure where else is good options for biophys/biochem. The US seems to have many strong institutes.

If anyone has any experience with these programs/institutes or have any information that could help I would very much appreciate it!

I want to apply for a PhD in biochemistry in future with a very specific interest in computational protein design (want to go to the institute for protein design at UW) . I need advices from someone with relevant experience. I am a Biomedical Engineering (BME) student with a minor in chemistry(almost double majored). Here are the courses that I will have completed by the end of my college studies. I have not listed all my courses, as several BME courses are not entirely relevant to this application.

Courses Completed by the Final Year of College

Major: Biomedical Engineering (BME) | Minor: Chemistry

Courses are 1 year based if not specified

Mathematics

• Calculus
• Engineering Mathematics (Differential Equations, Laplace Transformation, Fourier Transformation)

Programming

• Introduction to Python (1 semester)
• Introduction to Data Science (1 semester)
• Statistical Foundation of Machine Learning (1 semester)
• Introduction to Machine Learning using Python (1 semester)
• Introduction to Biostatistics with R (1 semester)

Biology

• General Biology (1 semester, human-focused)
• Molecular Biology
• Human Physiology

Chemistry

• General Chemistry
• General Chemistry Laboratory (1 semester)
• Organic Chemistry
• Analytical Chemistry
• Organic and Analytical Chemistry Laboratory
• Biochemistry
• Biochemistry Laboratory
• Physical Chemistry

Physics

• General Physics
• General Physics Laboratory (1 semester)

Biomedical Engineering (BME) Specific

• Introduction to Biomaterials (Metals, Ceramics, Polymers)

Writing a paper?

Re-running an experiment for the 18th time hoping you finally get results?

Analyzing some really cool data?

Start off your week by sharing your plans with the rest of us. å

I would like to know how an endo-acting hydrolases activity is understood and applied in enzyme reactions- the way I was taught is hydrolase activity is defined as the quantity of smaller units (i.e. glucose if using glucoamylase), but this seems to make sense only for exo-hydrolases. The endo enzymes will randomly choose internal linkages and I don't think there are many - if not at all - enzymes that act on specific lengths of polymers to yield consistent MW/DP of oligomers, or at least that was my experience. How do you exactly interpret the enzyme activity of endo-hydrolases?