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Topic: Protein folding


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 Learn more about Protein folding in the online encyclopedia.   (Site not responding. Last check: 2007-11-07)
In fact, disruption of the functional or "native" shapes of proteins is the primary cause of several neurodegenerative diseases, including those caused by prions and amyloid.
The particular amino-acid sequence of a protein predisposes it to fold into its native conformation, and many proteins do so spontaneously during or after their synthesis inside cells.
While these macromolecules may be seen as "folding themselves," in fact their folding depends a great deal on the characteristics of their surrounding solution, including the identity of the primary solvent (either water or lipid inside cells), the concentration of salts, and temperature.
www.onlineencyclopedia.org /p/pr/protein_folding.html   (539 words)

  
 Protein Folding
Although proteins are the most abundant biological substances in the animal kingdom, researchers don't have a very good picture of what they're like in all their diversity.
Contemporary protein scientists are a little like their brethren of the 16th century, who had heard rumors of exotic animals but didn't actually see them until voyages of discovery sent ships -- and collectors -- to distant lands.
In proteins, the tightly wound coils are in a "secondary" conformation, and the less regular loops of the coiled cord are in a "tertiary" conformation.
www.people.virginia.edu /~rjh9u/protfold.html   (3711 words)

  
 The Thermodynamics of Protein Unfolding
Another important aspect of protein structure is that native structures appear to be quite robust to mutations in their primary sequence with practically any residue in a sequence being replaceable without causing any change in the proteins structure or orientation.
The folded conformation of a domain is apparently in a relatively narrow free energy minimum, and substantial perturbations of that folded conformation require a significant increase in free energy.
Folded proteins demonstrate varying degress of flexibility, which is of direct relevance to protein folding, in that it reflects the free energy constraints on unfolding and refolding.
www.csn.ul.ie /~stephen/reports/unfolding.html   (3115 words)

  
 Protein Folding
The fact that protein synthesis and folding are accomplished in only a couple of minutes argues that only a few of these possible conformations can possibly be tried in the proteins attempt to achieve the state of lowest free energy.
When the denaturants are removed, the proteins refold to their original conformations, often with the recovery of greater than 90% of biological activity.
Proteins that have too many hydrophobic groups to completely bury in their interiors must have some of these groups on their surfaces.
class.fst.ohio-state.edu /FST822/lectures/Fold.htm   (2046 words)

  
 Protein folding models
Co-operativity in a folding process demonstrates that the stability of the folded state is greater than the sum of the energies of the weak interactions involved.
29] This represents the energy surface of a protein folding pathway as a funnel, with a diverse multitude of unfolded conformations at the rim, and a single global minimum representing the native folded conformation.
This leads to a ``new view'' of protein folding whereby many paths exist from the unfolded to native states, and a protein molecule may follow the steepest (fastest folding) path, or a more round-about route passing through several local minima (intermediates) and maxima (transition states).
www.sanger.ac.uk /Users/sgj/thesis/html/node6.html   (877 words)

  
 protein misfolding captured in computer simulation
While protein components -- amino acids -- actually interact from any angle and not merely 90 degrees, possibilities are so complicated (more than the number of atoms in the known universe for a chain of 100 amino acids) that theoretical intervention is required through use of simplified lattices.
A protein is "born" in a shape approximating that of a string or pearl necklace, and folds into the shape that determines its function.
Proteins are not "bad" in character but consider how they were raised: as a series of simple amino acids.
www.sandia.gov /media/fold.htm   (1342 words)

  
 Protein Folding and Secondary Structure Prediction   (Site not responding. Last check: 2007-11-07)
Proteins are the biological molecules that are the building blocks of cells and organs, and the biochemical processes required to keep living organisms alive are catalyzed and regulated by a particular category of proteins called enzymes.
Proteins are linear polymers of amino acids that fold into complex conformations dictated by the physical and chemical properties of the amino acid chain.
Protein folding is usually a spontaneous process, and often when a protein unfolds because of heat or chemical denaturation, it will be capable of refolding into the correct conformation, as soon as it is removed from the environment of the denaturant, meaning folding and unfolding under these circumstances are reversible.
cnx.org /content/m11116/latest   (1398 words)

  
 Protein Folding   (Site not responding. Last check: 2007-11-07)
To determine the native folded state of a protein given only the primary sequence of amino acids is referred to as the protein folding problem.
The ability to determine a protein's native folded state is becoming critical with the massive increase in genetic sequence discovery and hence protein primary structure.
Information concerning the native folded state of a protein has great potential in the elucidation of biochemical pathways and their implications in disorders and disease.
www.cs.sandia.gov /~rlwaymi/Proteinfolding/proteinfolding.html   (429 words)

  
 2004 GRC on Protein Folding Dynamics
Protein folding represents the premier case where this quantitative approach has been successful and is becoming an example for other fields in biology.
Protein folding research is a multifaceted field of inquiry addressing fundamental problems in: polypeptide energetics and dynamics; chaperone-assisted structure formation; protein structure prediction; protein design; single-molecule detection; and the role of protein folding in diseases.
New measurement techniques have provided insights into the earliest steps in protein folding; theoretical work has led to the "new view" of protein folding based on energy landscape theory and the funnel concept; and misfolded proteins are emerging as significant factors in a number of diseases.
www.grc.uri.edu /programs/2004/protfold.htm   (523 words)

  
 UCSB Press Release: "UCSB Physicist Devises Way to Observe Protein Folding "
Since proteins in the body perform different functions according to their shape, the folding process is considered a very important area of study.
Although proteins are composed of just 20 different building blocks (the amino acids), the process by which a given sequence of these components adopts its unique structure is complex and poorly understood.
Folding proteins are too small to view with a microscope, so the researchers used a method called Forster Resonance Energy Transfer, or FRET, to study them.
www.ia.ucsb.edu /pa/display.aspx?PKey=1042   (568 words)

  
 WATCHING A PROTEIN FOLD
For proteins, function follows from form — the grooves and crevices of its complex folds are what allow it to latch onto other molecules and carry out its biological role.
The result is a more complete view of how one protein folds — in effect, a look at what hasn't been seen before, and it offers precious new insight into the folding process.
To capture protein movement at a useful level of detail, the full set of these interactions must be recalculated every femtosecond (a millionth of a nanosecond) of protein time.
www.psc.edu /science/Kollman98/kollman98.html   (1523 words)

  
 Protein Folding
Proteins are fundamental building blocks of living cells and perform crucial tasks in living cells.
Determination of the tertiary structure of proteins from their particular sequences of constituent amino acids is critical because the biological functions of proteins are dependent on their tertiary structure.
The amino acid sequences of protein molecules are being discovered at an explosive rate using DNA sequencing method, which extracts the amino acid sequences from the genetic codes.
hpcio.cit.nih.gov /Folding.htm   (710 words)

  
 Protein Folding   (Site not responding. Last check: 2007-11-07)
By targeting the recombinant protein to subcellular regions of the cells, such as the endoplasmic reticulum, a favorable environment is created for its appropriate folding and assembly, thus increasing the amount of recombinant proteins produced.
So far, pharmaceutical proteins produced in plants can be classified into three groups: human biopharmaceutical proteins, including growth hormone, human serum albumin, β-interferon, and erythropoietin; recombinant antibodies such as IgG1 and IgM; and recombinant subunit vaccines, from the hepatitis B envelope proteins and the rabies virus glycoproteins to the cholera toxin B subunit.
In addition, 140 therapeutic proteins have been approved and 500 are in clinical trials, and it is expected that at least 50 biotherapeutics will come on to the market over the next few years.
www.proteindesign.com   (2030 words)

  
 Jayant Udgaonkar   (Site not responding. Last check: 2007-11-07)
During a protein folding reaction, an unfolded polypeptide chain bends, twists, turns, coils and loops into a very precise structure that lets the folded protein get to work in the cell.
The protein folding problem is to determine how structure develops as a protein folds, and to decipher the code relating amino acid sequence to three-dimensional structure.
Folding is initiated typically by millisecond mixing methods, but faster mixing methods with microsecond resolution, as well as laser flash-induced temperature-jump and pH-jump methods with nanosecond to microsecond resolution, are also being developed.
www.ncbs.res.in /~faculty/jayant.html   (382 words)

  
 Chem 200A PROTEIN FOLDING Fall 1991   (Site not responding. Last check: 2007-11-07)
Of especial interest is the relatively recent realization that there must be preferred routes of folding; that is, although the denatured state exists in a very large number of different conformations (substates), very rapidly a limited (or unique) pathway of folding is adopted.
The major experimental problem in studying protein folding is the rapidity of the reaction and the normally very low concentration of intermediates (reflecting the highly cooperative nature of folding).
Experimentally, the methods I outlined for monitoring protein stability are equally valid for monitoring protein folding, with a few exceptions such as calorimetry.
www.chemistry.ucsc.edu /~fink/200lecture/lecture15.htm   (1986 words)

  
 Scientists develop sophisticated new simulation method for protein folding
He emphasizes that this is the first time simulations that model how proteins reach their folded state have included individual water molecules and agreed quantitatively with experimental data.
Proteins are thousands of times smaller than the thickness of the human hair, and the fastest proteins fold in about a millionth of a second, Pande points out.
In fact, Rhee's simulation revealed a new mechanism in protein folding -- the "concurrent mechanism." This is a process whereby the protein squeezes out water molecules at the same time it collapses on itself.
www.stanford.edu /dept/news/pr/2004/pande2428.html   (705 words)

  
 HHMI News: Researchers Use Computers to Redesign Protein Folding   (Site not responding. Last check: 2007-11-07)
The re-engineered protein folds 100-times faster than the natural protein and has a folding pathway that is completely reversed.
Folding determines how proteins – first synthesized as long chains of amino acids – assume the three-dimensional architecture that enables them to function as enzymes and other key cellular components.
Baker and his colleagues chose protein G for their studies because it possesses considerable symmetry, with two hairpin-shaped backbone regions that flank a helical region of the protein.
www.hhmi.org /news/baker2.html   (770 words)

  
 Apple - Science - Noah Johnson
As part of a groundbreaking distributed computing experiment, Johnson and half a million other people are donating their spare computer capacity so Stanford can remotely simulate protein folding, an essential biochemical process that controls vital body functions.
When proteins don’t fold properly — think of origami gone wrong — they can poison the cells around them and trigger diseases such as Alzheimer’s, cystic fibrosis, an inherited form of emphysema and even many cancers.
But analyzing a protein’s possible folding steps as it crumples up into a 3-D knot is daunting task, even for a supercomputer, because the molecular backbone of a protein can fold in trillions of different ways.
www.apple.com /science/profiles/proteinfolding   (715 words)

  
 Projects
How proteins self-assemble into their native state (responsible for biological function) has been a much studied problem for over a decade.
The protein structure files that are sent out as work contain the Cartesian atomic coordinates of a protein.
Try to unravel a fundamental issue in the "protein folding problem" (which itself lies at the heart of a huge amount of modern biomedical research): the fact that thousands of different sequences can all form the same three-dimensional structure.
www.stanford.edu /group/pandegroup/projects.html   (767 words)

  
 Membrane Protein Folding and Stability
One broad thermodynamic principle underlies the structure and stability of membrane proteins: The thermodynamic cost of transferring charged or highly polar uncharged compounds into the oil-like hydrocarbon interior of bilayer membranes is very high.
Although these broad principles are sufficient for understanding the basic structural motifs of membrane proteins, the prediction of the detailed three-dimensional structure of membrane proteins from amino acid sequence requires a detailed structural and thermodynamic understanding of the interactions of proteins with lipid bilayers.
Even though the unfolded state is inaccessible, the energetics of the folding can be estimated from the difference between the virtual free energy of transfer of the unfolded state (calculated using the interfacial hydrophobicity scale) and the measured free energy of transfer of the folded peptide.
blanco.biomol.uci.edu /mp_assembly.html   (1380 words)

  
 Primer on the protein folding problem   (Site not responding. Last check: 2007-11-07)
These proteins are then the carriers of the message contained in the DNA: i.e., a certain pigment, which is a protein, is responsible for skin colour; another protein is responsible for eye colour.
Proteins are therefore the basic unit of life, and an understanding of their structure and function is necessary to understand how life works.
The goal is to fold up proteins from amino acid sequences which are easy to obtain (these days, the entire genome sequence for several organisms is available) into correct 3D structures (which are very few in number compared to the number of amino acid sequences), theoretically (using a computer to do the actual folding steps).
www.ram.org /research/pfp.html   (540 words)

  
 Science of Folding@Home
One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties.
Thus, protein folding can be seen as a connection between the genome (sequence) and what the proteins actually do (their function).
The molecule drawn is the current atomic configuration ("fold") of the protein being simulated on your computer.
folding.stanford.edu /science.html   (810 words)

  
 Chaperone-Mediated Protein Folding -- Fink 79 (2): 425 -- Physiological Reviews
That substrate protein dissociation precedes ATP hydrolysis was
a folding chamber with ADP confined to the cis-ring (26, 188,
release of folding substrates and the cochaperonin GroES.
physrev.physiology.org /cgi/content/full/79/2/425   (10961 words)

  
 Molecular Modeling of Proteins
The protein folding problem entails the mathematical prediction of (tertiary, 3-dimensional) protein structure given the (primary, linear) structure defined by the sequence of amino acids of the protein.
A smooth empirical potential is constructed for use in off-lattice protein folding studies.
Decoys 'R' Us, database of computer generated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real.
www.mat.univie.ac.at /~neum/protein.html   (870 words)

  
 Welcome to Blueprint   (Site not responding. Last check: 2007-11-07)
The Distributed Folding Project (DFP) is a distributed computing approach to study protein folding.
Using protein folding algorithms, billions of protein structures are generated and assigned an energy score.
The DFP has served as an ideal platform to test new protein folding algorithms and to improve existing algorithms.
www.blueprint.org /proteinfolding/distributedfolding   (135 words)

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