...1. collagen Major structural protein (285 kDa) of extracellular matrix. An unusual protein in amino acid composition (very rich in glycine (30%), proline, hydroxyproline, lysine and hydroxylysine; no tyrosine or tryptophan), structure (a triple-helical arrangement of 95-kDa polypeptides giving a tropocollagen molecule, dimensions 300×0.5 nm), and resistance to peptidases. Most types are fibril-forming with a characteristic quarter-stagger overlap between molecules producing an excellent tension-resisting fibrillar structure. Type IV, characteristic of basal lamina, does not form fibrils. Many different types of collagen are now recognized. Some are glycosylated (glucose–galactose dimer on the hydroxylysine), and nearly all types can be cross-linked through lysine side chains. 2. elastin Glycoprotein (70 kDa) randomly coiled and crosslinked to form elastic fibres that are found in connective tissue. Like collagen, the amino acid composition is unusual with 30% of residues being glycine and with a high proline content. Cross-linking depends upon formation of desmosine from four lysine side groups. The mechanical properties of elastin are poorer in old animals. 3. keratins Group of highly insoluble fibrous proteins (of high _-helical content) which are found as constituents of the outer layer of vertebrate skin and of skin-related structures such as hair, wool, hoof and horn, claws, beaks and feathers. Extracellular keratins are derived from cytokeratins, a large and diverse...
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...Structures, Biosynthesis and Biofunctions of Iron-sulfer proteins Yiming Chen, Brown University, May 11th, 2011 I. Introduction Iron-sulfur proteins are the proteins which contain iron-sulfur clusters, like sulfide-linked di-, tri-, and tetrairon centers with various oxidative states 1. An excess of 120 distinct types of enzymes and proteins are known to contain Fe-S clusters2. Iron-sulfur proteins are known for the role of the oxidation-reduction reactions of mitochondrial electron transportation. They are also discovered in a series of metalloproteins procedures, for example, ferredoxins 3, Coenzyme Qcytochrome c reductase 4, succinate-coenzyme Q reductase 5 and nitrogenase 6. The iron-sulfur proteins have many functions including catalysis, generate radicals, and also can play as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally some of the Fe-S proteins are able to regulate the gene expression. Furthermore, the discoveries of new iron-sulfur proteins and iron-sulfur clusters has led to lots of interests of their amazing functional and structural diversity, which reflects the versatility of both iron and sulfur in biochemical processes. Since these iron-sulfur proteins are vey common on the metabolic pathways of most organisms, it leads some scientific interests that iron-sulfur compounds had a significant role in the origin of life in the Iron-sulfur world theory 7. Thus theory claims that the early life on earth probaby formed on the...
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...Protein Structure Horacio Madera Western Governors University -C624 July 2, 2015 A. Original model of the essential amino acid Threonine. B. Original diagram of the different levels of protein structure. C. Original diagram demonstrating how a peptide bond is made through dehydration. D. Original diagram that demonstrates how a peptide bond is broken through hydrolysis. E. Explanation of the four forces that stabilize a protein’s structure at the tertiary level of protein structure. Disulphide bridges are form very strong covalent bonds that are found in between Sulphur atoms in the amino acid cysteine molecules. Ionic bonds occur between a carboxyl and amino group that is not involved in a peptide bond. Hydrogen bonds result from the bonding of an electronegative oxygen atom and electropositive H atom. Hydrogen bonds can occur in either –OH or –NH groups. Hydrophobic interactions are created from certain non-polar hydrophobic amino acids that move to the center of the protein and away from the watery medium. This results in twists or folds of the polypeptide chain. Toole, G., & Toole, S. 2004, p. 38. Essential As Biology for OCR ( ed.). Cheltenham, United Kingdom : Nelson Thornes Ltd. F. Bovine spongiform encephalopathy (BSE) at a molecular level. Part F-Disease at the Molecular Level * Bovine spongiform encephalopathy (BSE) is...
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...Chapter 11 * Principles of Membrane Transport * Given enough time, nearly all molecules will diffuse across a membrane * Smaller, hydrophobic/non polar molecules diffuse rapidly * Larger molecules, and charged ions move much slower * So mechanisms are needed * 2 Main types of Membrane Transport Proteins * Transporters * Bind to a specific solute and undergo shape change to move solute through membrane * Channels * Much more weakly interact with molecules * Create pores that allow specific molecules to pass through * Allows much more rapid transport * Passive/Facilitated Transport * Used by all channels and some transporters * This uses no energy and moves molecules “downhill,” with their electrochemical gradient * Active Transport * Used by transporters, here usually called pumps * Requires energy, ATP * Move molecules against the electrochemical gradient * Transporters and Passive Transport * Glucose Transport * Passive transport * Cooperative transport coupled with the transport of Na+ * Binds 2 Na+ and 1 glucose * The binding of either ligand, glucose or Na+, increases binding of the other. The concentration of Na+ outside the cell is greater, so the net movement transports more of both ligands into the cell. * Transporters and...
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... (Wolfe 2000) B. (Borges 2014) (Wolfe 2000a) (Wolfe 2000c) (Wolfe 2000b) C. (HudonMiller 2012) D. (HudonMiller 2012) E. Hydrophobic Interactions: Proteins are composed of amino acids that contain either hydrophilic or hydrophobic Rgroups. It is the nature of the interaction of the Rgroups in the water environment that plays the major role in shaping protein structure. The folded state of globular proteins is due to the balance between the opposing energy of hydrogen bonding between hydrophilic Rgroups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic Rgroups. As a result, certain hydrophobic amino acid Rgroups then drive them away from the exterior of proteins and into the interior. This force restricts how a protein may fold. (King 2003) Van der Waals Interactions: Protein folding is controlled by van der Wall forces. Van der Wall forces can be both attractive and repulsive. Attractive van der Waals forces involve the interaction among induced dipoles that arise from changes in the charge densities that occur between adjacent uncharged nonbonded atoms. Repulsive van der Waals forces involve the interactions that take place when uncharged nonbonded atoms come very close together but do ...
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...Japan. Abstract: The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank (http://www.rcsb.org/pdb/) returns only 93 hits (as of September 2007) and, the NCBI database (http://www.ncbi.nlm.nih.gov) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which...
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... Biological Crystallography ISSN 0907-4449 Protein imperfections: separating intrinsic from extrinsic variation of torsion angles Glenn L. Butterfoss,a Jane S. Richardsonb and Jan Hermansa* a Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA, and bDepartment of Biochemistry, Duke University Medical School, Durham, North Carolina 27710-3711, USA Correspondence e-mail: hermans@med.unc.edu In this paper, the variation of the values of dihedral angles in proteins is divided into two categories by analyzing distributions in a database of structures determined at a resolution of Ê 1.8 A or better [Lovell et al. (2003), Proteins Struct. Funct. Genet. 50, 437±450]. The ®rst analysis uses the torsion angle for the CÐC bond (11) of all Gln, Glu, Arg and Lys residues (`unbranched set'). Plateaued values at low B values imply a root-mean-square deviation (RMSD) of just 9 for 11 related to intrinsic structural differences between proteins. Extrapolation to high resolution gives a value of 11 , while over the entire database the RMSD is 13.4 . The assumption that the deviations arise from independent intrinsic and extrinsic sources gives $10 as the RMSD for 11 of these unbranched side chains arising from all disorder and error over the entire set. It is also found that the decrease in 11 deviation that is correlated with higher resolution structures is almost entirely a consequence of the higher percentage...
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...Student’s name Code+ course name Professor’s name University name City, State Date Introduction The purpose of the experiment was to test the free sulphydryl groups that may be important for the enzyme activities as well as the roles that the disulphide bonds plays n the stabilizing of the structure that is 3 dimensional of the enzymes and proteins. The latter purpose is vital in the study of proteins. The results for tube 2 showed that N= 6.588 and that tube 3 showed that N= 0.153 sulphide groups in the samples. Tube 2 contained Urea and sodium borohydrate. When the proteins were denatured partially, it meant that only part of it was converted to a form that is insoluble under the conditions which the native proteins are soluble. The insoluble fractions had the number of reactive SH as well as the S-S groups’ characteristics of the completely denatured proteins. This experiment introduces some methods for investigating and analyzing sulphydryl and disulphide groups in proteins. Materials and methods Measurement of Sulphide and Disulphide groups in a protein with DTNB Lysozyme solution at a concentration of 0.5 mg/ml was used here. Four test tubes were set up and they were labeled as 1, 2, 3 and 4. 1.44 gms of urea were added into the test tubes of 2, 3 and 4. 0.1ml of 0.1M EDTA was added to the each tube.Afterward, 1.0 ml o f Lysozyme solution was added to test tubes of 1, 2 and 3 and...
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...sequencing has led to generation of a lot of biological data which include protein sequences data. The full understanding of the biological roles of protein requires the knowledge of their structures. Experimental protein structure prediction methods consisting of x-ray crystallography and NMR spectroscopy are time consuming leaving a gap between generation of sequences and structure prediction. Computational approaches can be used to develop protein structure models which can be used for rational design of biochemical experiments which include site directed mutagenesis, protein stability and functional analysis of proteins. There are three computational approaches to three dimensional structure prediction namely homology modeling, threading and ab initio prediction (Xong, 2006). Homology modeling (comparative modeling) is a computational protein structure modeling technique used to build three dimensional (3D) models of proteins of unknown structure ( the target) on the basis of a sequence similarity to proteins of known structure (the template). Two conditions must be met to build a useful model, the similarity between the target sequence and template must be detectable and a substantially correct alignment between the target and the template should be calculated. Homology modelling is possible because small changes in protein sequence result in small changes in its 3D structures. The 3D structures of proteins in a family are more conserved than their sequences, therefore if similarity...
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...PubMed Abstract: Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer...
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...Protein Spy Researchers at Rice University have a method to rapidly trigger the universal tagging of proteins being produced by a cell. The tagging method they use is like a switch. They tag proteins with a controllable enzyme switch. This allows researchers to get a snapshot of proteins being produced by a cell at any time. This is a divide and conquer kind of strategy. What hypothesis was tested? The hypothesis that was tested was attach bio-orthogonal that is non-interfering an amino acids to transfer RNA. This gives a snapshot of total protein synthesis. How was it tested? They tested this hypothesis by using an azidonorleucine amino to tag proteins in Escherichia coli bacteria cells. The switch is controlled like a computer program. The switch only charges transfer RNA cells with azidonorleucine efficiently when the switch is synthesized and a chemical is present in the cell to flip the switch. Instead of physically separating a cell from a mixture to find the proteins being made, they can use this engineered switch to put what amounts to a fishhook on every proteins synthesized in a given cell....
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...Protein misfolding – hidden enemy of the brain Protein has always been a fundamental and irreplaceable biomolecule that builds up life. The studying of protein, proteomics, not only allow humans be aware of ourselves and the biosphere around us but also set the foundation for scientists to approach solutions for many human’s health problems. Among those many health issues, diseases that are associated with central nervous system raise the most concern. Many of these nervous disorders, surprisingly, are caused by the misfolding of our own human’s protein rather than any infectious virus or bacteria. Indeed, protein misfolding can bring about fatal aftermaths and consequences. One of them is very well-known deadly diseases, Creutzfeld- Jakob...
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...Four Forces that Stabilize a Protein’s Structure at the Tertiary Level There are several types of bonds and forces that hold a protein in its tertiary structure. Hydrophobic interactions contribute to the folding and shaping of a protein. The "R" group of the amino acid is either hydrophobic or hydrophilic. The amino acids with hydrophilic "R" groups will search for interactions with water, while amino acids with hydrophobic "R" groups will avoid water and clump towards the center protein. Hydrogen bonding in the polypeptide chain and between amino acid "R" groups helps to stabilize protein structure by holding the protein in the shape made by the hydrophobic interactions. Due to protein folding, ionic bonding can occur between the positively and negatively charged "R" groups that come in contact with one another. Folding can also result in covalent bonding between the "R" groups of cysteine amino acids, also known as a disulfide bridge (strongest bond). Van der Waals forces interactions help in the stabilization of protein structure. These interactions refer to to the attractive and repulsive forces that occur between molecules that become polarized. These forces contribute to the bonding that occurs between molecules. (Borges,2014) Bovine Spongiform Encephalopathy Mad cow disease or bovine spongiform encephalopathy is a deadly neurological disease that affects adult cattle. It is transmitted from animal to animal through contaminated food that contain infected central...
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...Biochemistry Task 2 Paul A. Lebeck 000490213 January 26, 2016 A. B. (Borges, 2014, Wolfe, 2015). C. (Wolfe, 2015). D. (Wolfe, 2015). E. The forces, bonds, and interactions by protein structures at the Tertiary level. There are Hydrophobic (nonpolar), Ionic bonds, Hydrogen (covalent) bonds, and Disulfide bonds, also called Disulfide Bridges. Hydrophobic are nonpolar bonds, meaning they cannot interact with water or aqueous solutions. Hydrophobic interactions will cause the protein to change shape to avoid making contact with such solutions. Considered weak bonds, but the proteins cluster tightly together on the interior of the protein, Van der Waals interaction take place between the proteins, again these are the weakest of the molecular bonds. Ionic Bonds are by definition bonds that are made up of charged particles. There are 20 Amino Acids, some with negatively charged terminals, some with positively charged terminals. This is a basic chemistry property that opposites attract. These are considered stronger bonds, but not the strongest. Next are hydrogen bonds. Considered stronger bonds than hydrophobic bonds, but weak compared to ionic and disulfide bonds. Hydrogen bonds are formed from Polar Covalent interactions. Two amino acids share a hydrogen electron and connect on the second amino acid oxygen atom. There must be a hydrogen donor on one amino acid, and a hydrogen acceptor on a second amino acid to complete the bond. The strongest...
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...1-16 Protein Motifs Protein motifs may be defined by their primary sequence or by the arrangement of secondary structure elements The term motif is used in two different ways in structural biology. The first refers to a particular amino-acid sequence that is characteristic of a specific biochemical function. An example is the so-called zinc finger motif, CXX(XX)CXXXXXXXXXXXXHXXXH, which is found in a widely varying family of DNA-binding proteins (Figure 1-49). The conserved cysteine and histidine residues in this sequence motif form ligands to a zinc ion whose coordination is essential to stabilize the tertiary structure. Conservation is sometimes of a class of residues rather than a specific residue: for example, in the 12-residue loop between the zinc ligands, one position is preferentially hydrophobic, specifically leucine or phenylalanine. Sequence motifs can often be recognized by simple inspection of the amino-acid sequence of a protein, and when detected provide strong evidence for biochemical function. The protease from the human immunodeficiency virus was first identified as an aspartyl protease because a characteristic sequence motif for such proteases was recognized in its primary structure. The second, equally common, use of the term motif refers to a set of contiguous secondary structure elements that either have a particular functional significance or define a portion of an independently folded domain. Along with the functional sequence motifs, the former are...
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