"quantum leap forward in understanding proteins" (physics, computers, format)

[Brian.Pearson]

In this ongoing quest, a group of Scripps Research Institute scientists, along with colleagues from the University of California, San Diego, (UCSD) have borrowed from physics to deliver one of those research rarities—an unmitigated success. The group has devised a computational method that, with remarkable accuracy, predicts how bacterial proteins fold and interact.


In the short term, this new capability, described in this week's Early Edition of the Proceedings of the National Academy of Sciences, should allow development of new antibiotics that target and block newly identified protein interactions vital to the survival of pathogenic bacteria. In the longer term, as the collective body of genomics data for humans and other animals grows, some version of the new technique may allow similar protein predictive capabilities for higher organisms, spawning a wealth of new and highly effective drug discovery options.

[xavierob82]

Proteins sure are an immensely fascinating subject. Truly one of nature's marvels as tiny, molecular machines. But I thought we already knew how proteins fold: they fold and vibrate into random configurations thousands of times per millisecond until they find their most stable shape, guided mostly by two things: entropy and whether their outlying molecules are attracted or repelled by water. They simply find their most "comfortable" shape.

On a related note, I found this fascinating electron microscope pic of the protein helicase, the protein responsible for unwinding DNA to be copied into RNA:




Simply awesome!

[K-Luv]

Originally Posted by xavierob82

Proteins sure are an immensely fascinating subject. Truly one of nature's marvels as tiny, molecular machines. But I thought we already knew how proteins fold: they fold and vibrate into random configurations thousands of times per millisecond until they find their most stable shape, guided mostly by two things: entropy and whether their outlying molecules are attracted or repelled by water. They simply find their most "comfortable" shape.

On a related note, I found this fascinating electron microscope pic of the protein helicase, the protein responsible for unwinding DNA to be copied into RNA:
!

I thought that transcriptase was responsible for the folding?

[rcarrillo]

Originally Posted by xavierob82

Proteins sure are an immensely fascinating subject. Truly one of nature's marvels as tiny, molecular machines. But I thought we already knew how proteins fold: they fold and vibrate into random configurations thousands of times per millisecond until they find their most stable shape, guided mostly by two things: entropy and whether their outlying molecules are attracted or repelled by water. They simply find their most "comfortable" shape.

We know the basic rules for how proteins fold. Its a layerd process from the primary structure (amino acid sequence) to secondary (sprials and sheets) tothe tertiary structure (3D shape). We also understand the process you described is what forms these and how it works for small sections.

The missing piece has been taking a long string of amino acids and predicting what the final 3-dimensional protein will look like. Its complicated in that other proteins, enzymes, or molecules sometimes help "nudge" the protein into a final state that it would not assume without their interactions during the process.

There has been a lot of work the last few years using super computers and networks of volunteers (folding@home and others) to try and come up with a a precise computer model. It would be a huge benefit, to be able to sequence a protein and know what the final shape will look like. Unfortunately the only way to know for sure is still to grow crystals and analyze the shape... which can be very difficult for some proteins.

Originally Posted by xavierob82

On a related note, I found this fascinating electron microscope pic of the protein helicase, the protein responsible for unwinding DNA to be copied into RNA:

Originally Posted by K-Luv

I thought that transcriptase was responsible for the folding?

Transcriptase is an enzyme that catalyzes the formation of RNA from DNA during transcription.

Helicase are members of a family of enzymes that catalyze the unwinding and seperation of DNA (or RNA) strands during replication as xavierob82 said. They also unwind DNA during transcription, recombination and repair. I remember there are quite a few different familes of helicases depending on the process for which the DNA needs to be unwound.