What is Protein folding: Definition and 13 Discussions

Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure.
Folding of many proteins begins even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure (Anfinsen's dogma).The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded, so that protein dynamics is important. Failure to fold into native structure generally produces inactive proteins, but in some instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by incorrect folding of some proteins, because the immune system does not produce antibodies for certain protein structures.Denaturation of proteins is a process of transition from the folded to the unfolded state. It happens in cooking, in burns, in proteinopathies, and in other contexts.
The duration of the folding process varies dramatically depending on the protein of interest. When studied outside the cell, the slowest folding proteins require many minutes or hours to fold primarily due to proline isomerization, and must pass through a number of intermediate states, like checkpoints, before the process is complete. On the other hand, very small single-domain proteins with lengths of up to a hundred amino acids typically fold in a single step. Time scales of milliseconds are the norm and the very fastest known protein folding reactions are complete within a few microseconds.Understanding and simulating the protein folding process has been an important challenge for computational biology since the late 1960s.

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  1. H

    Mathematical process for protein folding

    Hello, I am currently working on an idea for a possible future masters or PhD in cellular biology, however my idea is currently just a passion project. For it to work, I would need to learn how to predict and make a specific protein to do a specific function, in this instance I need to use it to...
  2. EFech

    How Do Configurational and Conformational Entropy Differ in Protein Folding?

    I have been reading about protein thermodynamics and found different types and models for entropy calculation before and after protein folding. I understand Vibrational, conformational, configurational entropy are some of the most studied "types" of protein folding entropy. My questions is...
  3. EFech

    What are the implications of quantum biology on cognitive computational models?

    I am a student and researcher interested in the mind, brain, related biological processes and emerging "mental" processes. I am interested in cognitive computational models, implementing new computational paradigms.
  4. BWV

    AI-Powered AlphaFold 2: Revolutionizing Protein Folding

    This is cool - AI is the future of biology, humans just arent smart enough https://deepmind.com/research/case-studies/alphafold https://predictioncenter.org/casp14/doc/presentations/2020_12_01_TS_predictor_AlphaFold2.pdf Deepmind trained on 100K proteins and is now in the second iteration of...
  5. epenguin

    Protein folding AI: "Will Change Everything"

    Google’s deep-learning program for determining the 3D shapes of proteins stands to transform biology, say scientists...
  6. cobalt124

    Protein Folding and NP-Completeness

    I'm looking to understand how protein folding has been shown to be NP-complete, but from the computational side rather than the biological side (if this is possible). Is there an analogous NP-complete problem that is similar? I read that self avoiding random walks might have something to do with...
  7. S

    Ionic bond strength in protein folding?

    Our text says that ionic bonds are much weaker in aqueous solutions than covalent bonds, due to the dissociative properties of most ionic compounds in water. I read elsewhere though, that in general, ionic bonds are stronger due to the increased polarity. So, in protein folding, when different...
  8. ZetaOfThree

    Current research on protein folding

    As a non-biologist, I'm curious: What are some things that current research on protein folding is focusing on? What are some current challenges that researchers are facing? I understand that the protein folding problem is a very important problem in the field of biophysics. Any experts on here?
  9. Simfish

    Will better knowledge of protein folding mean that we can predict rxns?

    These days, it seems that we all rely on trial and error in order to predict the biochemical reactions of new drugs (say, we want a drug to be a ligand, but we have to rely on trial and error to predict whether or not it will actually fit - plus - we also need trial and error to determine the...
  10. E

    String theory and 6D Yau-Calibi like protein folding?

    In string theory, a solution involving flat 10D space seems like a valid solution. The Universe could be described by a solution that is 10D space, all large and flat. Of course for string theory to describe our universe, 3D remain large and flat, and 6D or 7D are curled up in a Yau Calibi...
  11. J

    Protein folding thermodynamics

    My textbook’s explanation for spontaneous renaturation of defolded protein is this: “Although in defolded state protein has grater entropy, greater degree of disorder, it folds into original conformation (lower entropy), and this seems to be in collision with the II law of thermodynamics. But...
  12. J

    Thermodynamics of protein folding

    My textbook’s explanation for spontaneous renaturation of defolded protein is this: “Although in defolded state protein has grater entropy, greater degree of disorder, it folds into original conformation (lower entropy), and this seems to be in collision with the II law of thermodynamics. But...
  13. E

    Investigating Interplay between Protein Folding Frustrations and Motifs

    The following is the abstract to an article by Joan Emma Shea et al published in journal of chemical physics volume 113 number 17, 1 nov 2000 "The amino acid sequence and the folding motif are essential in determining the protein folding mechanism. The interplay between energetic...