Folding (chemistry) - Factbites

Folding (chemistry) - Factbites
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Topic: Folding (chemistry)

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	Cornell Chemistry Faculty Research -
		We have pioneered the study of gas phase protein folding with these techniques, showing in detail how solvent removal changes the well characterized native folding in solution.
		•Italian Academy of Sciences, XL •American Chemical Society: Analytical Chemistry; Chemical Instrumentation; Mass Spectrometry; Nichols Gold Medal
		For gaseous protein ions, electron capture dissociation only affects the backbone bonds, with negligible cleavage of the tertiary non-covalent bonding, providing direct conformational characterization, as provided also by photodissociation spectroscopy with a tunable OPO IR laser.
	www.chem.cornell.edu /faculty/index.asp?fac=37 (373 words)

	The Longevity Meme -- pointing the way to a longer, healthier life
		Folding@Home is a distributed computing project run under the auspices of the smart guys at the Stanford University Chemistry Department.
		The Folding@Home site includes some introductory pages to explain the science behind the work, and how the results are making a difference.
		The understanding gained by the Folding@Home team speeds up the search for therapies and cures for a number of important degenerative conditions of aging.
	www.longevitymeme.org /projects/use_folding_at_home.cfm (385 words)

	Protein Folding & Subunit Association (V.J. LiCata)
		The process of protein folding is currently one of the most compelling enigmas in biological chemistry, occupying the full attention of literally hundreds of laboratories.
		Folding and Assembly of the Catalytic Trimer of ATCase
		In the absence of ligands, the free energy of monomer unfolding is estimated to be 2 kcal/mole or less, while in the presence of ligands, isolated monomers are never even detected.
	biosci.cbs.umn.edu /~licata/pf.html (385 words)

	Slashdot Folding@Home - Yet Another Distributed Client
		Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a non-profit institution dedicated to science research and education.
		Hopefully the folding@home folks are aware of such algorithms, and are using them to reduce the need for inter-client communication.
		By using the MPE when computing forces on a particle, and doing operations to combine multipole expansions, the overall amount of computation can be reduced to an almost linear relationship with the number of particles.
	slashdot.org /science/00/09/26/2111216.shtml (5298 words)

	Tweakers Australia - Technology News, Reviews and Analysis
		Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a nonprofit institution dedicated to science research and education.
		One of their 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.
		Their group has developed a new way to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way - with a near linear speed up in the number of processors.
	www.tweakers.com.au /projects/projects.asp (487 words)

	Foresight Update 26 Page 2
		As Lehn writes: "The contribution of supramolecular chemistry to chemical synthesis has two main aspects: the production of the non-covalent supramolecular species themselves and the use of supramolecular features to assist in the synthesis of covalent molecular structures." Both of these options can create atomically precise components useful in molecular mechanisms.
		Since the catalysts that he shows have their geometry defined by covalent bonds rather than by the hydrophobic effects that contribute to the folding of protein enzymes, one might expect these new catalysts to be more useful in a machine phase environment than proteins are.
		Lehn writes: "Supramolecular catalysts are by nature abiotic chemical reagents that may perform the same overall processes as enzymes, without following the detailed pathway by which enzymes actually effect them or under the conditions in which enzymes do not operate.
	www.foresight.org /Updates/Update26/Update26.2.html (2272 words)

	Chemistry Using the pharmaceutical literature
		, Wiley, 2000- http://www3.interscience.wiley.com/cgi-bin/jhome/72510898 Mission is to integrate this wide and flourishing field, ranging from complex carbohydrates through peptides/ proteins to DNA/ RNA, from combinatorial chemistry and biology to signal transduction, from catalytic antibodies to protein folding, from bioinformatics and structural biology to drug design.
		Theory and Computation in Chemistry, Physics, and Molecular Biology, Wiley, 1967- http://www3.interscience.wiley.com/cgi-bin/jhome/29830 Quantum mechanical description of the structure and dynamics of atoms, molecules, and condensed matter, embodies theoretical studies and computer simulations of atomic and molecular systems and their interactions.
		ACS has long needed a computational chemistry journal aligned with the society's Division of Computers in Chemistry and the Theoretical Chemistry Subdivision of the Division of Physical Chemistry.
	www.genomicglossaries.com /content/chapterchemogenomics.asp (2272 words)

	Chemistry at BU - Biophysical Chemistry
		Protein folding, nucleic acid structure, biological electron transfer, and macromolecular dynamics are some of the topics investigated by this group of researchers, using both experiment and computation.
		Research in the Biophysical Chemistry explores the connections between physical chemistry and the chemical function of biological molecules.
		The major goal in these research projects is to elucidate the underlying fundamental chemistry and engineering principles and to use that insight to direct our creative and scientific efforts.
	www.bu.edu /chemistry/faculty/researchareas/biophysical.html (2272 words)

	Mary T. Rodgers
		The energetics of dissociation in partially solvated systems is being studied to enhance our understanding of the effect of solvation on biochemical processes, to provide insight into folding and conformational stability of biological macromolecules, the energetics of solvation and structural information on the solvated complex.
		To determine quantitative thermochemistry from kinetic energy dependent CID studies, a precise determination of the dissociation threshold is required.
		The threshold represents the endothermicity of dissociation i.e.
	chem.wayne.edu /~mrodgers (5833 words)

	Chemistry Homework, Activity Web of Naugatuck, Connecticut
		Science Is Golden - Learn basic chemistry principles with the Folding Table of Elements.
		pH Factor - Try out this virtual chemistry lab.
		Activity Web is a venture of DLD2000.com, LLC offering Reading Entertainment, Long Distance Services, Site Design, Mountain Laurel Sudbury School, and Marketing
	www.activityweb.com /homework/chemistry.asp (5833 words)

	Folding@home - Wikipedia, the free encyclopedia
		Accurate simulations of protein folding and misfolding enable the scientific community to better understand the development of many diseases, including Alzheimer's disease, BSE (mad cow disease), and cystic fibrosis.
		So far, the Folding@home project has successfully simulated folding in the 5-10 microsecond range—a time scale thousands of times larger than were previously thought possible.
		It was launched on October 1, 2000, and is currently managed by the Pande Group, within Stanford University's Chemistry department, under the supervision of Professor Vijay S. Pande.
	en.wikipedia.org /wiki/Folding_at_home (486 words)

	From the Cover: How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations -- Takagi et al. 100 (20): 11367 -- Proceedings of the National Academy of Sciences
		size of the cage, the stabilization is larger for a larger substrate.
		effect of caging may be to restrict conformational motion of
		It may be the case that the Anfinsen cage effect, the iterative
	www.pnas.org /cgi/content/full/100/20/11367 (486 words)

	Title page for ETD etd-03242005-141647
		By comparing the crystal structures of the host and its taco complex, we proved that folding is a necessary step during the formation of taco complexes.
		We demonstrate not only that bis(m-phenylene)-32-crown-10-based cryptands are powerful hosts for paraquat derivatives compared with the simple crown ether, but also that cooperative complexation can be obtained with the cryptand structure.
		Finally the application of several new and known recognition motifs in the preparation of a supramolecular poly[3]pseudrotaxane, and the first pseudorotaxane-type supramolecular star-shaped polymer, and the first supramolecular hyperbranched polymer was discussed.
	scholar.lib.vt.edu /theses/available/etd-03242005-141647 (486 words)

	Science Forums and Debate - Ladies and Gentlemen... GRID/UD SFN Style
		The United Devices Cancer Research Project will advance research to uncover new cancer drugs through the combination of chemistry, computers, specialized software, and organizations and individuals who are committed to fighting cancer.
		United Devices has begun a new and exciting research project -- the Human Proteome Folding Project -- in collaboration with the Institute for Systems Biology, the University of Washington, and IBM Corporation.
		As such, the promise of understanding the complete set of human proteins, what their structures are and how they interact in the human body is a hugely important scientific problem that could lead to treatments for a myriad of human diseases.
	www.scienceforums.net /forums/printthread.php?t=7117 (486 words)

	Tweakers Australia - Technology News, Reviews and Analysis
		Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a nonprofit institution dedicated to science research and education.
		One of their 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.
		Their group has developed a new way to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way - with a near linear speed up in the number of processors.
	www.tweakers.com.au /projects/projects.asp (487 words)

	Ralf Warmuth - Rutgers Chemistry and Chemical Biology Department
		Host-Guest Chemistry; Supramolecular Chemistry; Design and Synthesis of Molecular Container Compounds; Inner Phase Chemistry and Catalysis (Chemistry and Catalysis Inside Molecular Container Compounds); Reactive Intermediates; Strained Hydrocarbons; De Novo Design of Helical Peptides; Conformationally Constrained Amino Acids; Peptide-based Ion-Channels; Photochemical Triggers for Protein Folding
		Chemistry and Properties of Cycloheptatetraene Inside a Hemicarcerand.
		Inclusion Phenomena and Molecular Recognition in Chemistry, 2000, 37, 1-38.
	chmwww.rutgers.edu /faculty/warmuth.html (487 words)

	Folding@home scientists report first distributed computing success
		"The process of protein folding remains a mystery," said Pande, assistant professor of chemistry and of structural biology at Stanford.
		With 30,000 computers at their disposal, Pande and Snow were able to perform 32,500 folding simulations and accumulate 700 microseconds of folding data.
		Two years ago, Pande launched Folding@home — a distributed computing project that so far has enlisted the aid of more than 200,000 PC owners, whose screensavers are dedicated to simulating the protein-folding process.
	www.eurekalert.org /pub_releases/2002-10/su-fsr_2102102.php (748 words)

	Frank Potter's Science Gems - Physical Science III
		Organic Compounds Database - compiled by H. Bell at Virginia Tech and hosted by the Department of Chemistry, Colby College, Waterville, Maine Large Database (Text & Images).
		Protein Folding, Dynamics and Function - H. Roder, Fox Chase Cancer Center "...the kinetics and energetics of folding for several well-characterized proteins, including cytochrome c, ubiquitin and staphylococcal nuclease, as well as natural and engineered variants of these proteins."
		Molar Mass/Percent by Mass Calculator - D. Woodcock, Department of Chemistry, Okanagan University College, B.C., Canada Enter formula.
	www.sciencegems.com /physical3.html (4156 words)

	Biophysics
		Biophysics 164r, Molecular Biophysics and Biophysical Chemistry: Simulation of Macromolecules (offered alternate years as Chemistry 164r), is an introduction to the principles of macromolecular structure, folding and dynamics, with emphasis on structure-function relationship.
		The program is administered by the Committee on Higher Degrees in Biophysics, which is comprised of senior representatives from the Departments of Biological Chemistry and Molecular Pharmacology; Molecular and Cellular Biology; Chemistry and Chemical Biology; Physics; Genetics and Pathology.
		Biophysics 242, Special Topics in Biophysics, invites two or more professors in the spring term to speak on new areas of their own research, thereby introducing students to new questions and methods of research that would not normally be accommodated by the regular curriculum.
	www.gsas.harvard.edu /programs/degree/biophys.html (4156 words)

	Biophysics
		Biophysics 164r, Molecular Biophysics and Biophysical Chemistry: Simulation of Macromolecules (offered alternate years as Chemistry 164r), is an introduction to the principles of macromolecular structure, folding and dynamics, with emphasis on structure-function relationship.
		The program is administered by the Committee on Higher Degrees in Biophysics, which is comprised of senior representatives from the Departments of Biological Chemistry and Molecular Pharmacology; Molecular and Cellular Biology; Chemistry and Chemical Biology; Physics; Genetics and Pathology.
		Biophysics 242, Special Topics in Biophysics, invites two or more professors in the spring term to speak on new areas of their own research, thereby introducing students to new questions and methods of research that would not normally be accommodated by the regular curriculum.
	www.gsas.harvard.edu /programs/degree/biophys.html (3554 words)

	Molecules: Editor and Editorial Board
		Keywords: enzyme inhibitors, heterocycles, isotopically-labeled compounds, Lewis acids and bases, quninoxaline N-oxides, photochemistry, ESR, aromaticity, molecular recognition, protein folding, thermodynamics, symmetry, entropy, nature of chemical processes
		Keywords: Supramolecular chemistry, heterocyclic chemistry, especially sulfur-containing heterocycles, tetrathiafulvalene chemistry, macrocyclic chemistry, macrocyclic ligands, cyclophanes, rotaxanes and catenanes of donor-acceptor type
		Keywords: Heterocycles, fused ring and nitrogen; Nitrogen containing compounds, amines, poliamines, isocyanates and hydrazines; Addition reaction, pseudo-Michael; Carbonyl reactions, acylation, nucleophylic addition and other condensations, synthesis of biologicaly (especially CNS) active compounds, SAR of the opioid receptors, molecular modeling of the small drug-like molecules, identification of their physical properties, affecting pharmacological activity
	www.mdpi.org /molecules/editors.htm (4609 words)

	Ars Food Court :: Distributed computing mayhem
		Earlier this month, Professor Vijay S. Pande, PhD, the Director of the Folding@Home Distributed Computing Project, and Assistant Professor of Chemistry and of Structural Biology, Stanford University, formally announced the project would be developing a Folding client based on Berkeley's Open Infrastructure for Network Computing (BOINC).
		A closed beta is currently collecting data from core members of the BOINC and Folding projects, with an open beta test of the client to be announced in the coming weeks.
		The article notes the Pande Group has been working with David Anderson's group at Berkeley for more than a year, presumably (IMO) while the BOINC DC platform continued to evolve and mature to a point where it would support the unique needs of the Folding project.
	www.arsfoodcourt.com (2340 words)

	Apple - Science - Noah Johnson
		Vijay Pande, a professor of chemistry and structural biology at Stanford, saw the potential for thousands of desktop computers to calculate tiny portions of a folding sequence.
		When the application is running on a Mac or other computer, Pande’s software pulls simulation packets from Stanford servers, makes folding calculations on the Mac and reports the results back to the Stanford server.
		With its ability to share the workload among hundred of thousands of computers economically, Folding@home can help scientists understand how proteins snap, or don’t, into their predestined shapes — and may help to explain the origins of diseases such as Alzheimer’s and apparently unrelated diseases.
	www.apple.com /science/profiles/proteinfolding (715 words)

	Wired News: Genome Effort Hits Home
		Genome@home is the second project from Stanford University's chemistry department, which also runs the Folding@Home project.
		"I personally will certainly learn a lot more on how to design sequence," said John Desjarlais, assistant professor of chemistry at Penn State University, who co-wrote some of the code in the Genome@Home program and plans to work with data generated from the program.
		Whereas Folding@Home is designed to learn how genomes fold into proteins, Genome@Home was launched this week to try and reverse engineer known proteins by guessing the genome sequence of their structures.
	www.wired.com /news/technology/0,1282,41842,00.html (715 words)

	Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
		Since formation of a distinct tertiary structure is critical for obtaining catalytic activity, folding is at the heart of understanding structure−function relationships in ribozymes.
		The only modification that we have identified that permits formation of the closed complex without proceeding to cleavage is the modification of the 2'-OH group in the substrate, which functions intimately in the reaction chemistry as the attacking nucleophile.
		Further similarities between the two systems are suggested by recent studies on the dynamics of the P4-P6 domain, involving reversible docking of subdomains separated by a flexible hinge between separately folding subdomains of the molecule, with the inactive conformer consisting of a species in an extended form with coaxial stacking interactions (Szewczak and Cech, 1997).
	www.nature.com /cgi-taf/DynaPage.taf?file=/emboj/journal/v17/n8/full/7590948a.html (9270 words)

	The Center for Theoretical Biological Physics
		The workshop is designed primarily for people with undergraduate or higher degrees in the physical sciences (physics, chemistry, and engineering) with an interest into moving into areas of biological physics.
		The lectures will cover six main areas: the nature of biological structures; development and use of molecular force fields; simulation methods; statistical thermodynamics; electrostatics; and energy landscapes in protein folding and structure prediction.
		Computational experiments will be drawn from a variety of application areas (including protein folding, electron transfer events, ligand docking, enzymatic reaction mechanisms, structure refinement, multi-scale modeling, and biomolecular visualization), and participants are encouraged to bring their own ideas for projects.
	ctbp.ucsd.edu /workshopinfo_2004.html (9270 words)

	The Center for Theoretical Biological Physics
		The workshop is designed primarily for people with undergraduate or higher degrees in the physical sciences (physics, chemistry, and engineering) with an interest into moving into areas of biological physics.
		Computational experiments will be drawn from a variety of application areas (including protein folding, electron transfer events, ligand docking, enzymatic reaction mechanisms, structure refinement, multi-scale modeling, and biomolecular visualization), and participants are encouraged to bring their own ideas for projects.
		The lectures will cover six main areas: the nature of biological structures; development and use of molecular force fields; simulation methods; statistical thermodynamics; electrostatics; and energy landscapes in protein folding and structure prediction.
	ctbp.ucsd.edu /workshopinfo_2004.html (435 words)

	Internet-based Distributed Computing Projects - Active Projects
		Folderol is a volunteer project that uses a screensaver, command-line client or system client application to simulate protein folding of the data from the Human Genome Project.
		United Devices' second project is searching for cancer-fighting drugs in partnership with the National Foundation for Cancer Research (NFCR) Centre for Drug Discovery in the Department of Chemistry at the University of Oxford, England.
		Folding@home is another volunteer project that uses a screensaver or client application based on the Mithral CS-SDK to simulate protein folding in an effort to better understand how proteins self-assemble or fold.
	distributedcomputing.info /distrib-2001/distrib-projects.html (4255 words)

	Sulfhydryl group - Wikipedia, the free encyclopedia
		The chemistry of the sulfhydryl group is thus related to the chemistry of alcohols; thiols form thioethers, thioacetals and thioesters, in which the alcohol-derived oxygen atom is replaced by a sulfur atom in the oxygen-analogous compounds ethers, acetals, and esters.
		When the sulfhydryl groups of two cysteine residues (as in monomers or constituent units) are brought near each other in the course of protein folding, an oxidation reaction can create a cystine unit with a disulfide bond (-S-S-).
		In organic chemistry, a sulfhydryl group or thiol group is a functional group composed of a sulfur and a hydrogen atom (-SH).
	en.wikipedia.org /wiki/Sulfhydryl_group (368 words)

	Georgia Tech, School of Biology
		Marta Garcia-Ramirez, Feng Dong, and Juan Ausio (1992) "Role of the histone 'tails' in the folding of oligonucleosomes depleted of histone H1", Journal of Biological Chemistry 267 19587-19595.
		Feng Dong, Edward P. Gogol, and Peter H. von Hippel (1995) "The phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate", Journal of Biological Chemistry 270, 7462-7473.
		Feng Dong and Peter H. von Hippel (1996) "The ATP-activated helicase hexamer of bacteriophage T4 (gp41) forms a stable primosome with a monomer of T4-coded primase (gp61)", Journal of Biological Chemistry 271, 19625-19631.
	www.biology.gatech.edu /dong.html (846 words)

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