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    Protein

    Being vegetarian does not mean your diet will be lacking in protein. Most plant foods contain protein and in fact it would be very difficult to design a vegetarian diet that is short on protein. Excess dietary protein may lead to health problems. It it now thought that one of the benefits of a vegetarian diet is that it contains adequate but not excessive protein. Proteins are made up of smaller units called amino acids. There are about 20 different amino acids, eight of which must be present in the diet. These are the essential amino acids. Unlike animal proteins, plant proteins may not contain all the essential amino acids in the necessary proportions. However, a varied vegetarian diet means a mixture of proteins are consumed, the amino acids in one protein compensating for the deficiencies of another.

    Structure & Functions

    Proteins are highly complex molecules comprised of linked amino acids. Amino acids are simple compounds containing carbon, hydrogen, oxygen, nitrogen and occasionally sulphur. There are about 20 different amino acids commonly found in plant and animal proteins. Amino acids link together to form chains called peptides. A typical protein may contain 500 or more amino acids. Each protein has it's own unique number and sequence of amino acids which determines it's particular structure and function. Proteins are broken down into their constituent amino acids during digestion which are then absorbed and used to make new proteins in the body. Certain amino acids can be made by the human body. However, the essential amino acids cannot be made and so they must be supplied in the diet. The eight essential amino acids required by humans are: leucine, isoleucine, valine, threonine, methionine, phenylalanine, tryptophan, and lysine. For children, histidine is also considered to be an essential amino acid.

    Proteins are essential for growth and repair. They play a crucial role in virtually all biological processes in the body. All enzymes are proteins and are vital for the body's metabolism. Muscle contraction, immune protection, and the transmission of nerve impulses are all dependent on proteins. Proteins in skin and bone provide structural support. Many hormones are proteins. Protein can also provide a source of energy. Generally the body uses carbohydrate and fat for energy but when there is excess dietary protein or inadequate dietary fat and carbohydrate, protein is used. Excess protein may also be converted to fat and stored.

    Source from: vegsoc.

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    Search Proein


    The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

    Additional protein information

    search proeinIn addition to Protein sequences, other protein-related information is available via Entrez. Search the Structure database by choosing, "Structure" from the Entrez pull down menu, Conserved Domains Database (CDD) by choosing, "Domains",and 3D Domains by choosing, the "3D Domains" option.

    Retrieve taxonomy information

    The Entrez protein database is cross-linked to the Entrez taxonomy database.This allows you to find taxonomy information for the species from which a protein sequence was derived. First, look up a protein in Entrez. A "Taxonomy"link appears to the right of each entry that is linked to the Entrez taxonomy database. To view all non-redundant taxonomy links for a search result, select "Taxonomy Links" from the drop-down menu above the search results and click on the "Display" button to the left of that menu.

    Molecule of the Month

    Nerve cells need to be able to send messages to each other quickly and clearly.One way that nerve cells communicate with their neighbors is by sending a burst of small neurotransmitter molecules. These molecules diffuse to the neighboring cell and bind to special receptor proteins in the cell surface. These receptors then open, allowing ions to flow inside. The process is fast because the small neurotransmitters, such as acetylcholine or serotonin, diffuse rapidly across the narrow synapse between the cells. The channels open in milliseconds, allowing ions to flood into the cell. Then, they close up just as fast, quickly terminating the message as the neurotransmitters separate and are removed from the synapse.suorce from: ncbi.nlm.nih.gov

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    Protein Information Reource

    protein information reourceSince 1984, PIR has produced the Protein Sequence Database (PSD) of functionally annotated protein sequences, which grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Now a part of the UniProt effort, sequences and annotations in PIR-PSD have been integrated into UniProt Knowledgebase. Release 80.00 (31-Dec-2004) is the final release for PSD. iProClass, central point for exploration of protein information, provides summary descriptions of protein family, function and structure for PIR-PSD, Swiss-Prot, and TrEMBL sequences, with links to over 90 biological databases . Release 2.79, 17-Oct-2005, contains 2307,958 entries. PIR-NREF, a mprehensive database for sequence searching and protein identification, contains non-redundant protein sequences from PIR-PSD, Swiss-Prot, TrEMBL, RefSeq, GenPept, and PDB.

    Molecular Visualization Freeware Protein Explorer

    Protein Explorer, a RasMol-derivative, is the easiest-to-use and most powerful software for looking at macromolecular structure and its relation to function. And it's free! It runs on Windows or Macintosh/PPC computers. (linux users see below.) RasMol users will find its menus very familiar, and it understands RasMol commands. It is very fast: rotating a protein or DNA molecule shows its 3D structure. If you have never seen this, watch the image at the upper right of this page. (Click here to see another molecule rotate.) Look at our gallery to see still snapshots of other molecules. Also available here are Chime-based tutorials on

    The Principles of Protein Structure

    Birkbeck College's Advanced Certificate in the Principles of Protein Structure using the Internet is a tutor assisted course accredited by the University of London. The course exploits modern developments in communications, which means that students from any country may study the course at home, at work or in your university. It is of one year duration and of final year undergraduate/postgraduate standard.

    The course co-ordinator is Dr Jim Pitts. Dr. Clare Sansom is the principal tutor and course material developer.The course runs for one year between November and October. We are still accepting applications for the 2005-6 course.

    Click here for More information, and how to apply If you would like more information about the course please email the course administrator, Maureen Austin Successful completion of the one year PPS course can be used as a qualifying course to undertake a further years' study leading to the MSc in Structural Biology using the internet. Click the link for further details of this option.
    Source from: pps.cryst.bbk.ac.uk

    About HPRD

    Commercial entities may not use this site without prior licensing authorization. please send an e-mail for further information about licensing. the Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.

    Please cite the following reference for this database: Peri, S. et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research. 13:2363-2371.

    The Candida Albicans Physical Map Website

    The completion of the 10.7x sequence of the Candida albicans genome and its annotation has provided Candida researchers with important tools for the analysis of this important human pathogen. However, since the sequence has not yet been finished and there is no genetic map, ordering and assignment to chromosomes of contigs and their genes cannot be accomplished without a physical map. The extensive heterozygosity found in strain SC5314, whose genome was sequenced, may have important biological consequences. In order to provide information and tools to address these needs and problems, a physical map, based on a fosmid library, is being constructed, and a Single Nucleotide Polymorphism (SNP) map, based on Assembly 19 of the genome, is available.

    ICE (the Institute for Candida Experimentation) at the University of Minnesota is an informal group of geneticists and cell biologists who work on Candida albicans. The group includes the laboratories of Judith Berman, Dana Davis, Cheryl Gale, David Kirkpatrick, and Bebe and Pete Magee.

    Candida Albicans And Its Genome

    candida albicans and its genomeCandida albicans is the most frequently isolated fungal pathogen of humans, affecting immuocompromised patients ranging from premature infants to AIDS sufferers. Systemic infections have an attributed mortality of 30-50%. Although many properties have been shown to contribute to virulence in animal studies, its pathogenesis is not well understood. Analysis of the genome has been undertaken to provide researchers with more tools to investigate Candidiasis.

    C. albicans is a diploid organism which has eight sets of homologous chromosomes. Its genome size is about 16 Mb (haploid), about 30% greater than S. cerevisiae (baker’s yeast). In 1996, the Stanford Genome Technology Center undertook the sequencing of the C. albicans genome with the funding provided by the Burroughs Wellcome Fund and the National Institute for Craniofacial and Dental Research. Sequencing was completed to a level of 10.7x in 2003. Diploid and haploid assemblies are available at. Source from: albicansmap.ahc.umn.edu

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    Protein Explorer Copyright

    Protein Explorer is offered as unsupported freeware. All use is at the risk of the user. No warranty whatsoever is made or implied. This version is free for all users, but downloaded copies or derivatives thereof may not be publically redistributed on CD's, served from publically-accessible websites, or publically redistributed by other means without permission. Permission is given to link to Protein Explorer freely from other websites, provided no fee is charged for access. Permission is given to distribute Protein Explorer locally to students within a class or educational institution, from a nonpublic intranet server, or via CD, provided no fee is charged. Supported by the Division of Undergraduate Education of the National Science Foundation, and the University of Massachusetts. Co-Authors and Acknowledgements.

    PDB ID Codes & Files

    One Molecule: To see a molecule in Protein Explorer (PE), you must first choose an atomic coordinate file (often called a PDB file) that contains the 3D structure of the molecule. (Protein Explorer cannot calculate the 3D structure of a protein from the amino acid sequence -- see Nature of 3D Structure Data.) Each PDB file has a unique 4-character identification code. Examples: 2HHD (hemoglobin), 1BL8 (potassium channel). If you don't know the PDB ID code you want, see below to find it. After you find the PDB code you want, enter it in the slot above.

    Explore the Membership Benefits of The Protein Society!

    The Protein Society welcomes individuals devoted to furthering research and development in protein science to apply for a regular or corporate membership. Members have an opportunity to actively participate in the emerging fields of protein science including proteomics, bioinformatics, structural biology, and computational biology as they pertain to proteins at the molecular and cellular level.

    PepTalk: The Protein Information Week

    CHI is pleased to present its Fifth Annual PepTalk event. PepTalk 2006 is packed with presentations from industry leaders, poster sessions presenting the latest research, over 50 exhibitors showcasing the latest technologies and expanded networking opportunities. To register and for more information visit.

    Protein Science November Issue

    Protein Science is dedicated to research on all scientific aspects of protein molecules. The journal publishes papers by leading scientists from all over the world that report advances in the understanding of proteins in the broadest sense. Visit the journal website at proteinscience.org to view the latest published research.

    Renew your membership dues for 2006 today to maintain uninterrupted service of the journal, Protein Science. New Benefit Being Offered This Year! Corresponding Authors are entitled to receive one free 4-color figure per article in Protein Science.

    The Protein Society's corporate members represent a partnership for progress, future growth, development and innovation through access to the best technical talent in the field.

    Public Affairs

    The Protein Society helps keep its members current on relevant legislation and science policy issues. Through its membership in FASEB, the Society has participated in advocating for funding support of NIH and NSF, and other relevant agencies. As a member of the Bridging the Sciences Coalition, the Society advocates for increased funding at the interface between the life sciences and physical sciences.

    Representatives from the nation's leading not-for-profit medical/scientific societies and publishers announced their commitment to providing free access and wide dissemination of published research findings.
    Source from: proteinsociety.org

    Protein Wisdom

    He "the one last post before I go and drink myself silly post" post Two things. First, go visit SPC Jean-Paul Borda’s milblogging.com/, which currently boasts links to 478 military blogs in 15 countries. The site is searchable by country, by gender, and by author. If you like what you see, bookmark it or add it to your RSS feed.

    And second, as a way to prepare myself for my ascension to the nation’s High Court, I’ve been working on writing material for narrowly defined demographics—a mental exercise that I hope will sharpen my conservative restraint and focus (I tend to wander, which is evident to those of you who read me with any regularity—a habit of mine that tends to manifest itself in long, compound complex sentences whose clauses tie together like strings of poorly-formed and badly polished pearlettes. But I digress.)

    Protein families database of alignments and HMMs

    protein families database of alignments and hmmsPfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. For each family in Pfam you can:

    • Look at multiple alignments
    • View protein domain architectures
    • Examine species distribution
    • Follow links to other databases
    • View known protein structures

    For more information on Pfam, on using this site, or on the changes between Pfam releases 17.0 and 18.0, click here. Pfam can be used to view the domain organisation of proteins. A typical example is shown below. Notice that a single protein can belong to several Pfam families.75% of protein sequences have at least one match to Pfam. This number is called the sequence coverage and is shown in the pie chart on the right.

    Pfam is a database of two parts, the first is the curated part of Pfam containing over 7973 protein families. To give Pfam a more comprehensive coverage of known proteins we automatically generate a supplement called Pfam-B. This contains a large number of small families taken from the PRODOM database that do not overlap with Pfam-A. Although of lower quality Pfam-B families can be useful when no Pfam-A families are found.

    Database of Macromolecular Movements

    This describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.

    Explore the database

    use our software Browse the database through the hierarchy of motions. Entries are organized by type of motion and by CATH classification. View a sortable list of of all movies, some of which are tarballed here Recent submissions are displayed first. The highlights page showcases some of our best movies. Samuel Flores's 2005 article in "The Pharma Frontier" explains molecular motions to the public.

    Use our software

    If you want to make your own movies, we have a Morph Server that will interpolate between any two protein conformations. We have also developed servers for Helical Interaction Analysis in proteins and for Normal Mode Analysis of protein domains. Want to predict hinges in your protein? We have a NEW FlexOracle Hinge Prediction Server that will predict hinges from a single structure.Many useful programs for structure analysis produced by members of the lab are available for download.
    Source from: molmovdb.mbb.yale.edu

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    Protein Synthesis

    what are proteinsProcess whereby DNA encodes for the production of amino acids and proteins.This process can be divided into two parts:

    1. Transcription Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can be described as a unit of three nucleotides called a codon.

    2. Translation The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. During this stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA. At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome.

    What Are Proteins?

    Proteins are necklaces of amino acids --- long chain molecules. Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions which make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?

    Further Studies

    In the decades after Anfinsen's work, the National Institutes of Health and the National Science Foundation continued to finance research in several laboratories. Working in relative obscurity, these protein biochemists tried to discover how a completely unfolded protein, with hundreds of millions of potential folded states to choose from, consistently found the correct one—and did so within seconds to minutes.

    Could there be specific, critical intermediates (partially folded chains) in the folding process? This turned out to be a difficult question to answer. Partially folded chains don't stay that way very long; they become fully folded chains in a fraction of a second. Nevertheless, by the early 1980s researchers had not only found clear evidence for the existence of partially folded proteins, but also realized the key role these played in the folding process.

    One study involved the difficulty in getting bovine growth hormone to fold properly. Although the unfolded proteins were not sticky, and the fully folded proteins were not sticky, the partially folded molecules stuck to each other—a first clue as to the origins of misfolded lumps (at least for purified proteins in test tubes). It still remained unclear why misfolding occurred in cells under certain circumstances but not under others.

    Why Do Proteins "Fold"?

    However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."

    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. Movies of the results of some of these simulation results can be found here.

    Protein Folding And Disease: Bse (Mad Cow), Altzheimer's

    What happens if proteins don't fold correctly? Diseases such as Alzheimer's disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding.

    When proteins misfold, they can clump together ("aggregate"). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimer's disease.

    Protein Folding And Nanotechnology

    protein folding and nanotechnologyIn addition to biomedical applications, learning about how proteins fold will also teach us how to design our own protein-sized nanomachines" to do similar tasks. Of course, before nanomachines can carry out any activity, they must also be assembled.

    Why Is Protein Folding So Difficult To Understand?

    It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate.

    In fact, it takes about a day to simulate a nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds). Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result!

    What Have We Done So Far And Where Are We Going?

    has been a success. We have folded several small, fast folding proteins, with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions.Since then, Folding@Home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, Trp Cage, among others. More recently, we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer's, Hunntington's, and Osteogenesis Imperfecta.You can learn more about our results, on our Results Page and you can see specific , peer-reviewed scientific achievements on our Papers Page. suorce from: proteinwisdom.com

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    Unraveling the Mystery of Protein Folding

    This series of essays was developed as part of FASEB's efforts to educate the general public, and the legislators whom it elects, about the benefits of fundamental biomedical research particularly how investment in such research leads to scientific progress, improved health, and economic well-being.

    Alzheimer's disease. Cystic fibrosis. Mad Cow disease. An inherited form of emphysema. Even many cancers. Recent discoveries show that all these apparently unrelated diseases result from protein folding gone wrong. As though that weren't enough, many of the unexpected difficulties biotechnology companies encounter when trying to produce human proteins in bacteria also result from something amiss when proteins fold.

    What exactly is this phenomenon? We all learned that proteins are fundamental components of all living cells: our own, the bacteria that infect us, the plants and animals we eat. The hemoglobin that carries oxygen to our tissues, the insulin that signals our bodies to store excess sugar, the antibodies that fight infection, the actin and myosin that allow our muscles to contract, and the collagen that makes up our tendons and ligaments (and even much of our bones)—all are proteins.

    To make proteins, `machines' known as ribosomes string together amino acids into long, linear chains. Like shoelaces, these chains loop about each other in a variety of ways (i.e., they fold). But, as with a shoelace, only one of these many ways allows the protein to function properly. Yet lack of function is not always the worst scenario. For just as a hopelessly knotted shoelace could be worse than one that won't stay tied, too much of a misfolded protein could be worse than too little of a normally folded one. This is because a misfolded protein can actually poison the cells around it.

    `Gunking Up' Tissues

    As far back as the start of this century, physicians have been noticing that certain diseases are characterized by extensive protein deposits in certain tissues. Most of these diseases are rare, but Alzheimer's is not. It was Alois Alzheimer himself who noted the presence of "neurofibrillary tangles and neuritic plaque" in certain regions of his patient's brain. Tangles are more or less common in diseases that feature extensive nerve cell death; plaque, however, is specific to Alzheimer's. The major question, which has only recently been answered, is whether plaque causes Alzheimer's or, like tangles, is a consequence of it.

    Further investigation showed that neuritic plaque (unrelated to the plaque that clogs atherosclerotic blood vessels and causes heart attacks) is composed almost entirely of a single protein. Deposits of large amounts of a single, insoluble protein around the degenerating nerve cells of Alzheimer's disease eventually provided a key to understanding the disorder.

    It was development of the biotechnology industry that unexpectedly spurred interest in insoluble protein gunk. This industry can produce proteins (often otherwise difficult-to-obtain human proteins) quickly and economically in bacteria. To their surprise, however, scientists who worked for biotech companies often found two things: protein that was supposed to be soluble instead precipitated as insoluble inclusion bodies within the bacteria and proteins that were supposed to be secreted into the surrounding medium instead got stuck at the bacterial cell wall.This puzzling activity led scientists, almost for the first time, to seriously study just what goes wrong during protein folding.

    Further Studies

    unraveling the mystery of protein foldingIn the decades after Anfinsen's work, the National Institutes of Health and the National Science Foundation continued to finance research in several laboratories. Working in relative obscurity, these protein biochemists tried to discover how a completely unfolded protein, with hundreds of millions of potential folded states to choose from, consistently found the correct one—and did so within seconds to minutes.

    Could there be specific, critical intermediates (partially folded chains) in the folding process? This turned out to be a difficult question to answer. Partially folded chains don't stay that way very long; they become fully folded chains in a fraction of a second. Nevertheless, by the early 1980s researchers had not only found clear evidence for the existence of partially folded proteins, but also realized the key role these played in the folding process.

    One study involved the difficulty in getting bovine growth hormone to fold properly. Although the unfolded proteins were not sticky, and the fully folded proteins were not sticky, the partially folded molecules stuck to each other—a first clue as to the origins of misfolded lumps (at least for purified proteins in test tubes). It still remained unclear why misfolding occurred in cells under certain circumstances but not under others.

    Temperature Sensitivity

    The early 1980s also saw one of the first serious investigations of protein misfolding. These studies focused on temperature-sensitive mutations (mutations allowing growth at 75-F but not at 100-F) in the tailspike protein of bacteriophage P22. Neither bacteriophage P22, a virus that infects certain bacteria, nor its tailspike protein has any practical importance in themselves. Faced with thorny problems, however, scientists often look for experimental systems that will allow them to get a foothold or find a way around them. In this case, they thought that a large protein, whose folding passes through multiple stages, would be a good system for looking at folding pathways within cells. Many temperature-sensitive mutations had already been isolated in bacteriophages, but never examined for their effect on folding.

    Their hopes were realized: The majority of the temperature-sensitive mutations they found, despite having only one amino acid altered, caused the tailspike protein to end up as insoluble gunk at high temperatures. Since these folding failures were occurring in bacterial cells that were growing in the laboratory, it was now possible to analyze what went wrong in a protein's folding process.
    Source from: faseb.org


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