DOCSLIB.ORG

A REVIEW of the HIGHER-ORDER STRUCTURES and APPLICATIONS of COLLAGEN MIMETIC PEPTIDES a Thesis Presented to the Graduate Facul

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A REVIEW of the HIGHER-ORDER STRUCTURES and APPLICATIONS of COLLAGEN MIMETIC PEPTIDES a Thesis Presented to the Graduate Facul A REVIEW OF THE HIGHER-ORDER STRUCTURES AND APPLICATIONS OF COLLAGEN MIMETIC PEPTIDES A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Polymer Science Max Goldmeier May 2016 A REVIEW OF THE HIGHER-ORDER STRUCTURES AND APPLICATIONS OF COLLAGEN MIMETIC PEPTIDES Max Goldmeier Thesis Approved: Accepted: ______________________________ ______________________________ Faculty Advisor Dean of the College Dr. Nita Sahai Dr. Eric J. Amis ______________________________ ____________________________ Faculty Co-Advisor Dean of the Graduate School Dr. William J. Landis Dr. Chand Midha ______________________________ ____________________________ Department Chair Date Dr. Coleen Pugh ii ABSTRACT Collagen is a protein that is a major component of the human body and makes up thirty percent of the total protein in the human body. Collagen mimetic peptides (CMPs) have been used to study the formation of the triple helix of collagen and its higher- ordered structures. This article discusses how CMPs have been used to learn about the physical properties of the triple helix and how the amino acid sequence affects the physical properties, formation, and stability of the triple helix. CMPs have also been designed to form higher-ordered structures for various applications. This work reviews the design principles and strategies employed with various interactions to form higher- ordered structures from CMPs. These strategies include the use of electrostatic interactions, the incorporation of cysteine knots, and metal-induced self-assembly, among others. Many of these higher-ordered structures have applications such as biomolecule attraction, cellular adhesion, nanowire fabrication, and hydrogel formation. iii DEDICATION This work is dedicated to my family for their support and encouragement. iv ACKNOWLEDGEMENTS I would like to thank Dr. Nita Sahai and Dr. William Landis from the Department of Polymer Science at The University of Akron in Akron, OH for their guidance and support which made this work possible. v TABLE OF CONTENTS Page LIST OF TABLES…………………………………………………………………...…viii LIST OF FIGURES………………………..……………………......................................ix CHAPTER I. INTRODUCTION……………………………………………………..………………..1 1.1 Introduction………………………………………………...………………….1 1.2 Features of Collagen and Biosynthetic Process of Collagen Formation………5 II. HELICAL TWIST OF THE TRIPLE HELIX OF COLLAGEN…………………….10 III. TRIPLE HELIX STABILITY AND AMINO ACID SEQUENCE… ………….…..13 3.1 Introduction to Collagen Triple Helix Stability……………………………...13 3.2 Tertiary Amides……………………………………………………………...14 3.3 Stereoelectronic Effects……………………………………………………...15 3.4 Hydrogen Bonding…………………………………………………………...17 3.5 Electrostatic Interactions……………………………………………………..18 3.6 The Role of Glycine in Triple Helix Stability……………………………….19 3.7 Conclusion of Triple Helix Stabilizing Factors……………………………...21 IV. HIGHER-ORDER CMP STRUCTURES……………….............................………..22 4.1 Intro to Higher-Order Structure and Applications of CMPs…………………22 4.2 Pro-Hyp-Gly CMPs………………………………………………………….23 vi TABLE OF CONTENTS (CONT.) Page 4.3 Pro-Pro-Gly CMPs…………………………………………………………...24 4.4 CMP Amphiphiles…………………………………………………………...29 4.5 2+1 Strand Click Synthesis…………………………………………………..34 4.6 Cysteine Bridges……………………………………………………………..36 4.7 Aromatic Interactions………………………………………………………...38 4.8 Metal-Induced Self-Assembly……………………………………………….41 4.9 Electrostatic Interactions……………………………………………………..47 4.10 Nanodiamond-CMP Conjugates……………………………………………52 4.11 Polymerized-CMPs and CMP-Dendrimers…………………………………52 V. CONCLUSION ………………………………………………………………………59 VI. BIBLIOGRAPHY……………………………...…………………………………….61 vii LIST OF TABLES Table Page 1. Chart displaying the types of collagen, their classification, distribution, and pathology.2, 3………………………………………………………………….……2 2. The amino acid composition of type I collagen α1and α2 chains that form the type I collagen triple helix. The Pro-Hyp-Gly sequence (the corresponding amino acids are in bold) is the highest occurring sequence in the chains.1 Amino acids are organized by highest content in the α1(I) chain to lowest………………………...6 3. The stability effects of tertiary amides in comparison to POG and PPG sequences. Tertiary amides other than Nleu tend to have a destabilizing effect on the Tm of CMP triple-helices……………………………………………………………….14 4. Stereoelectronic effects contribute to the stability of the triple helix as shown by the use of fluorinated derivatives of proline. Tm values from Ref. 2……………16 5. Acp and Fmp were used to show that even though a residue may not have the appropriate ring puckering for the position it is in, the hydrogen bonding network can provide stability to the triple helix. Tm values from Ref. 45………………...18 viii LIST OF FIGURES Figure Page 1. Schematic of the biosynthesis of collagen. Genetic coding for collagen is transcribed to form a protocollagen strand. The protocollagen strand undergoes enzymatic modification to form a procollagen triple helix. Proteinases trim the N- and C-termini thus producing a tropocollagen triple helix which self-assembles into fibrils that cross-link to form fibers.2, 6 Reprinted with permission from Shoulder, MD, Raines, RT, Annual Review of Biochemistry, 2009, 78, 929-958 © 2009, Annual Reviews………………………………………………………….7 2. TEM and AFM images of collagen displaying D-periodicity. A) TEM of collagen fibrils from human Achilles tendon stained with gold-palladium. Scale bar = 500 nm. B) TEM of type I collagen from calk-skin stained with phosphotungstic acid. Scale bar = 100 nm. C) AFM image of corneal collagen fibrils. Scale bar = 100 nm. D) AFM image of scleral collagen fibrils. Scale bar = 100nm. A, B) Adapted with permission from Electron Microscopy Reviews, 3/1, Chapman, JA, et al., The collagen fibril – a model system for studing the staining and fixtion of a protein, 143-182 © 1990 with permission from Elsevier. C, D) Adapted with permission from Japanese Journal of Ophthalmology, 46/5, Yamamto, S, Hitomi, J, et al., Observation of human corneal and scleral collagen fibrils by atomic force microscopy, 496-501 © 2002 with permission from Elsevier…………………….8 3. A scheme of the helical twist and unit height parameters. In a 72 helical twist, there are 21 amino acids that constitute two turns of the helix and a unit height of 20 Å. Reprinted with permission from Biopolymers, 84/4, Okuyama, K, Wu, G, et al., Helical twists of collagen model peptides, 421-432 © 2006 John Wiley and Sons………………………………………………………………………………11 4. Cϒ-endo and Cϒ-exo ring puckering of the pyrrolidine ring residues. Proline or proline derivatives with Cϒ-endo ring puckering in the X position and Cϒ-exo ring puckering in the Y position provide stability to the collagen triple helix through stereoelectronic effects. These stereoelectronic effects orient the main chain dihedral angles of the collagen chain to form a triple helix…………….………..15 ix LIST OF FIGURES (CONT.) Figure Page 5. A schematic diagram of a one-residue stagger and interchain hydrogen bonding between three strands (dashed line) that enables triple helix formation in procollagen and (POG)n CMPs…………………………………………………..17 6. CMP design with a Gly→Ala substitution.49 This CMP mimics the defective collagen found in patients suffering from OI…………………………………….20 7. TEM of (POG)10 and polyPOG. A) (POG)10 with branched extensive branching of 64 65 the fibers. B) (POG)10 aggregates of nanofibers. C) poly-POG fibers 65 displaying higher dispersion of fibers than (POG)10. A) Reprinted with permission from The Journal of Biological Chemistry, 281/44, Kar, K, Amin, P, et al., Self-association of collagen triple helic peptides into higher order structures, 33283-33290 © 2006 American Society for Biochemistry and Molecular Biology B, C) Adapted with permission from Biopolymers, 79/3, Kishimoto, T, Morihara, Y, et al., Synthesis of poly (Pro–Hyp–Gly)n by direct polycondensation of (Pro–Hyp–Gly)n, where n= 1, 5, and 10, and stability of the triple‐helical structure, 163-172 © 2005 John Wiley and Sons……………….…25 8. TEM of nanofibers from a CMP with the sequence (GPP)3GPR-GEKGER- 72 GPR(GPP)3-GPCCG at different scales. A, B) Scale bar = 0.5 μm and C, D) Scale bar = 1μm. Reprinted with permission from Biomacromolecules, 32/7, Krishna, O. D., and Kiick, K. L., Integrin-mediated adhesion and proliferation of human MSCs elicited by a hydroxyproline-lacking, collagen-like peptide, 6412- 6424 © 2009 American Chemical Society........................................................…26 9. A) Schematic of PPG CMP F877. The underlined G at position 901 was substituted with Ser in the G901S CMP. B) TEM of F877 nanofibers. Scale bar = 40 nm. C) TEM of G901S fibers. Scale bar = 40nm. Adapted with permission from Angewandte Chemie International Edition, 46/18, Bai, H, Xu, K, et al., Fabrication of Au nanowires of uniform length and diameter using a monodisperse and rigid biomolecular template: collagen‐like triple helix, 3383- 3386 © 2007 John Wiley and Sons…………………………...………………….27 x LIST OF FIGURES (CONT.) Figure Page 10. A) TEM of the cubes assembled by streptavidin-labelled gold nanoparticles and a biotinylated F877 CMP. Scale bar = 1μm. B) TEM of the hexagonal structures that assembled when the diameter of the gold nanoparticles was raised to 30 nm. Scale bar = 1μm. Adapted with permission from Angewandte Chemie International Edition, 49/45, Kaur, P, Maeda, Y, et al., Three‐dimensional directed self‐assembly of peptide nanowires into micrometer‐sized crystalline cubes with
Load more

Recommended publications
  • Collagen and Elastin Fibres
    J Clin Pathol: first published as 10.1136/jcp.s3-12.1.49 on 1 January 1978. Downloaded from J. clin. Path., 31, Suppl. (Roy. Coll. Path.), 12, 49-58 Collagen and elastin fibres A. J. BAILEY From the Agricultural Research Council, Meat Research Institute, Langford, Bristol Although an understanding of the intracellular native collagen was generated from type I pro- biosynthesis of both collagen and elastin is of collagen. Whether this means that the two pro- considerable importance it is the subsequent extra- collagens are converted by different enzyme systems cellular changes involving fibrogenesis and cross- and the type III enzyme was deficient in these linking that ensure that these proteins ultimately fibroblast cultures, or that the processing of pro become the major supporting tissues of the body. type III is extremely slow, is not known. The latter This paper summarises the formation and stability proposal is consistent with the higher proportion of collagen and elastin fibres. of soluble pro type III extractable from tissue (Lenaers and Lapiere, 1975; Timpl et al., 1975). Collagen Basement membrane collagens, on the other hand, do not form fibres and this property may be The non-helical regions at the ends of the triple due to the retention of the non-helical extension helix of procollagen probably provide a number of peptides (Kefalides, 1973). In-vivo biosynthetic different intracellular functions-that is, initiating studies showing the absence of any extension peptide rapid formation of the triple helix; inhibiting intra- removal support this (Minor et al., 1976), but other cellular fibrillogenesis; and facilitating transmem- workers have reported that there is some cleavage brane movement.
    [Show full text]
  • 01. Amino Acids
    01. Amino Acids 1 Biomolecules • Protein • Carbohydrate • Nucleic acid • Lipid 2 peptide polypeptide protein di-, tri-, oligo- 3 4 fibrous proteins proteins globular proteins 5 Figure 4.1 Anatomy of an amino acid. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure. 6 Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V)* Leucine (Leu, L)* Isoleucine (Ile. I)* 7 Serine (Ser, S) Threonine (Thr, T)* Cysteine (Cys, C)cystine Methionine (Met, M)* 8 Aspartate (Asp, D) Glutamate (Glu, E) Asparagine (Asn, N) Glutamine (Gln, Q) 9 Lysine (Lys, K)* Arginine (Arg, R)* 10 Phenylalanine (Phe, F)* Tyrosine (Tyr, Y) Histidine (His, H)* Tryptophan (Trp, W)* 11 Proline (Pro, P) 12 Hydrophobic (A, G, I, L, F, V, P) Hydrophilic (D, E, R, S, T, C, N, Q, H) Amphipathic (K, M, W, Y) 13 Essential amino acids: V, L, I, T, M, K, R, F, H, W 14 Several Amino Acids Occur Rarely in Proteins We'll see some of these in later chapters • Selenocysteine in many organisms • Pyrrolysine in several archaeal species • Hydroxylysine, hydroxyproline - collagen • Carboxyglutamate - blood-clotting proteins • Pyroglutamate – in bacteriorhodopsin • GABA, epinephrine, histamine, serotonin act as neurotransmitters and hormones • Phosphorylated amino acids – a signaling device Several Amino Acids Occur Rarely in Proteins Several Amino Acids Occur Rarely in Proteins Figure 4.4 (b) Some amino acids are less common, but nevertheless found in certain proteins. Hydroxylysine and hydroxyproline are found in connective-tissue proteins; carboxy- glutamate is found in blood-clotting proteins; pyroglutamate is found in bacteriorhodopsin (see Chapter 9).
    [Show full text]
  • Collagen Structural Microheterogeneity and a Possible Role for Glycosylated Hydroxylysine in Type 1 Collagen
    Proc. NatL Acad. Sci. USA Vol. 79, pp. 7684-7688, December 1982 Biochemistry Collagen structural microheterogeneity and a possible role for glycosylated hydroxylysine in type 1 collagen (nonreducible stable crosslinks/hydroxyaldolhistidine/specific cleavage/molecular location) MITSUO YAMAUCHI*t, CLAUDIA NOYES*t, YOSHINORI KUBOKI*t, AND GERALD L. MECHANIC*§¶ *Dental Research Center, §Department of Biochemistry and Nutrition, and tDepartment of Medicine, University of North Carolina, Chapel Hill, North Carolina 27514 Communicated by. Ernest L. Eliel, September 20, 1982 ABSTRACT A three-chained peptide from type I collagen, and Mechanic (8) that dehydro-HisOHMerDes, which was crosslinked by hydroxyaldolhistidine, has been isolated from a thought to be artifactual (9, 10) is a true crosslink in collagen tryptic digest of5 M guanidine HCI-insoluble bovine skin collagen fibrils. Bernstein and Mechanic found that one HisOHMerDes (a small but as yet unknown percentage of the total collagen in crosslink was present per molecule of collagen in freshly re- whole skin). Os04/NaIO4 specifically cleaved the crosslink at its constituted soluble collagen fibrils. double bond into a two-chained crosslink peptide and a single pep- Histidine was also found to be a constituent of the stable tide. The sequence of the two-chained peptide containing the bi- nonreducible trifunctional crosslink hydroxyaldolhistidine functional crosslink was determined after amino acid analysis of (OHAlHis), whose structure was elucidated by PMR and mass the separated peptides. The crosslink consists of an aldehyde de- spectrometry rived from hydroxylysine-87 in the aldehyde-containing cyanogen (11). OHAIHis was isolated from bovine skin col- bromide fragment alCB5ald and an aldehyde derived from the lagen.
    [Show full text]
  • United States Patent (19) 11 Patent Number: 5,874,589 Campbell Et Al
    USOO5874589A United States Patent (19) 11 Patent Number: 5,874,589 Campbell et al. 45) Date of Patent: Feb. 23, 1999 54 METHODS FOR SYNTHESIZING DIVERSE El Marini et al., 1992, Synthesis pp. 1104-1108 Synthesis of COLLECTIONS OF TETRAMIC ACIDS AND enantiomerically pure B-and Y-amino acids from aspartic DERVATIVES THEREOF and glutamic acid derivatives. Evans et al., 1982, J. Amer. Chem. Soc. 104: 1737–1739 75 Inventors: David A. Campbell, San Mateo; Todd Asymmetric alkylation reactions of chiral imide enolates. A T. Romoff, San Jose, both of Calif. practical approach to the enantioselective Synthesis of C-Substituted carboxylic acid derivatives. 73 Assignee: GlaxoWellcome, Inc., Research Fontenot et al., 1991, Peptide Research, 4: 19-25A Survey Triangle Park, N.C. of potential problems and qulaity control in peptide Synthe sis by the flourenylmethocvarbonyl procedure. 21 Appl. No.: 896,799 Giesemann et al., 1982, J. Chem. Res. (S) pp. 79 Synthesis 22 Filed: Jul.18, 1997 of chiral C-isocyano esters and other base-Sensitive isocya nides with 51) Int. Cl. ........................ C07D 211/40; CO7D 207/00 oxomethylenebis-(3H-Imidazolium)Bis(methanesulphonate), 52 U.S. Cl. ............ ... 548/540; 546/220; 548/539 a versatile dehydrating reagent. 58 Field of Search ............................. 546/220; 548/539, Geysen et al., 1987, J. Immunol. Meth. 102: 259-274 548/540 Strategies for epitope analysis using peptide Synthesis. Giron-Forest et al., 1979, Analytical Profiles of Drug Sub 56) References Cited stances, 8: 47-81 Bromocriptine methaneSulphonate. U.S. PATENT DOCUMENTS Gokeletal, 1971, Isonitrile Chemistry, Ugi, I. ed., Academic 3,299.095 1/1967 Harris et al.
    [Show full text]
  • Ihyd-Pseaac: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity Into Pseudo Amino Acid Composition
    Int. J. Mol. Sci. 2014, 15, 7594-7610; doi:10.3390/ijms15057594 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition Yan Xu 1,5,*, Xin Wen 1, Xiao-Jian Shao 2, Nai-Yang Deng 3 and Kuo-Chen Chou 4,5 1 Department of Information and Computer Science, University of Science and Technology Beijing, Beijing 100083, China; E-Mail: [email protected] 2 Department of Mathematics and Information Science, Binzhou University, Binzhou 256603, China; E-Mail: [email protected] 3 College of Science, China Agricultural University, Beijing 100083, China; E-Mail: [email protected] 4 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; E-Mail: [email protected] 5 Gordon Life Science Institute, Boston, MA 02478, USA * Author to whom correspondence should be addressed; E-Mail: [email protected] or [email protected]; Tel./Fax: +86-10-6233-2589. Received: 7 February 2014; in revised form: 4 April 2014 / Accepted: 17 April 2014 / Published: 5 May 2014 Abstract: Post-translational modifications (PTMs) play crucial roles in various cell functions and biological processes. Protein hydroxylation is one type of PTM that usually occurs at the sites of proline and lysine. Given an uncharacterized protein sequence, which site of its Pro (or Lys) can be hydroxylated and which site cannot? This is a challenging problem, not only for in-depth understanding of the hydroxylation mechanism, but also for drug development, because protein hydroxylation is closely relevant to major diseases, such as stomach and lung cancers.
    [Show full text]
  • Lysyl-Protocollagen Hydroxylase Deficiency in Fibroblasts from Siblings with Hydroxylysine-Deficient Collagen
    Proc. Nat. Acad. Sci. USA Vol. 69, No. 10, pp. 2899-2903, October 1972 Lysyl-Protocollagen Hydroxylase Deficiency in Fibroblasts from Siblings with Hydroxylysine-Deficient Collagen (prolyl-protocollagen hydroxylase/connective tissue/inborn error/crosslinks) S. M. KRANE, S. R. PINNELL, AND R. W. ERBE Departments of Medicine, Dermatology, and Pediatrics, Harvard Medical School and the Medical, Dermatology, and Children's Services, Massachusetts General Hospital, Boston, Massachusetts 02114 Communicated by E. R. Blout, July 31, 1972 ABSTRACT Cell culture studies were performed on were normal. The hydroxylysine content of dermis was also members of a family in which two sisters, ages 9 and 12, normal in three patients, each with the Marfan and Ehlers- have a similar disorder characterized clinically by severe scoliosis, joint laxity and recurrent dislocations, hyper- Danlos syndromes. Collagen from the skin of the affected extensible skin, and thin scars. The skin collagen from the children was more soluble in denaturing solvents than that sisters was markedly deficient in hydroxylysine, but other derived from controls (4), consistent with a defect in cross- amino acids were present in normal amounts. Hydroxy- linking of collagen molecules, a process in which hydroxylysine lysine in collagen from fascia and bone was reduced to a to involved lesser extent. Since the most likely explanation for the has been thought be critically (2, 5-8). Hydroxyly- hydroxylysihie deficiency was a reduction in enzymatic sine per se is not used in collagen biosynthesis; specific lysyl hydroxylation of lysine residues in protocollagen, we mea- residues are hydroxylated after their incorporation into the sured the activity of lysyl-protocollagen hydroxylase in polypeptide chains of protocollagen (9-12).
    [Show full text]
  • Lysine and Novel Hydroxylysine Lipids in Soil Bacteria: Amino Acid Membrane Lipid Response to Temperature and Ph in Pseudopedobacter Saltans
    Rowan University Rowan Digital Works School of Earth & Environment Faculty Scholarship School of Earth & Environment 6-1-2015 Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans Elisha Moore Rowan University Ellen Hopmans W. Irene Rijpstra Irene Sanchez Andrea Laura Villanueva See next page for additional authors Follow this and additional works at: https://rdw.rowan.edu/see_facpub Part of the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Moore, E.K., Hopmans, E., Rijpstra, W.I.C., Sanchez-Andrea, I., Villanueva, L., Wienk, H., ...& Sinninghe Damste, J. (2015). Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans. Frontiers in Microbiology, Volume 6, Article 637. This Article is brought to you for free and open access by the School of Earth & Environment at Rowan Digital Works. It has been accepted for inclusion in School of Earth & Environment Faculty Scholarship by an authorized administrator of Rowan Digital Works. Authors Elisha Moore, Ellen Hopmans, W. Irene Rijpstra, Irene Sanchez Andrea, Laura Villanueva, Hans Wienk, Frans Schoutsen, Alfons Stams, and Jaap Sinninghe Damsté This article is available at Rowan Digital Works: https://rdw.rowan.edu/see_facpub/17 ORIGINAL RESEARCH published: 29 June 2015 doi: 10.3389/fmicb.2015.00637 Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans Eli K. Moore 1*, Ellen C. Hopmans 1, W. Irene C. Rijpstra 1, Irene Sánchez-Andrea 2, Laura Villanueva 1, Hans Wienk 3, Frans Schoutsen 4, Alfons J.
    [Show full text]
  • Reducible Crosslinks in Hydroxylysine-Deficient Collagens of a Heritable Disorder of Connective Tissue (Skin/Bone/Cartilage/Aminoacid Analysis)
    Proc. Nat. Acad. Sci. USA Vol. 69, No. 9, pp. 2594-2598, September 1972 Reducible Crosslinks in Hydroxylysine-Deficient Collagens of a Heritable Disorder of Connective Tissue (skin/bone/cartilage/aminoacid analysis) DAVID R. EYRE AND MELVIN J. GLIMCHER* Department of Orthopedic Surgery, Harvard Medical School, Children's Hospital Medical Center, Boston, Massachusetts 02115 Communicated by Francis 0. Schmitt, July 3, 1972 ABSTRACT Reducible compounds that participate don, bone, and cartilage collagens (3-11). Each tissue reveals in crosslinking were analyzed in hydroxylysine-deficient a unique distribution of these reducible crosslinks that changes collagens of patients with a heritable disorder of connec- tive tissue. After treatment with [3H1sodium borohydride, as the tissue matures and ages (8, 10). new compounds, as well as a totally different pattern of Since connective tissues of patients with this disorder are tritiated compounds, were found in hydroxylysine-de- deficient in hydroxylysine, a crosslink precursor, it seemed ficient collagen from skin as compared with age-matched likely that the reducible crosslinks would either be absent or controls. The amount of desmosines detected indicated collagen cross- that more elastin was present in abnormal skin than in abnormal. Such a deficiency or abnormality in control skin. linking might be responsible for changes in the solubility Bone collagen, which was not as deficient in hydroxy- characteristics of the collagen (1), and for changes in the lysine as skin collagen, had the same compounds as normal structural properties of the tissues and the consequent skeletal bone collagen, but their relative proportions were altered, and connective tissue abnormalities. consistent with a deficiency of hydroxylysine, a precursor of the crosslinks.
    [Show full text]
  • Biochemistry Centennial Celebration 1915 - 2015
    BIOCHEMISTRY CENTENNIAL CELEBRATION 1915 - 2015 FEATURED SPEAKERS Dr. Hung-Ying Kao (Ph.D., 1995) Dr. Rebecca Moen (Ph.D., 2013) Professor of Biochemistry Assistant Professor of Chemistry & Geology Case Western Reserve University | Cleveland, OH Minnesota State University | Mankato, MN Dr. Venkateswarlu Pothapragada (Ph.D., 1962) Dr. Amy Rocklin (Ph.D., 2000) Division Scientist, 3M | Minneapolis-St. Paul, MN Corning, Inc. | Painted Post, NY Dr. Melanie Simpson (Ph.D., 1997) Dr. Brad Wallar (Ph.D., 2000) Professor of Biochemistry Associate Professor of Chemistry University of Nebraska | Lincoln, NE Grand Valley State University | Allendale, MI Thursday, May 14, 2015, 1:00-5:30 PM 2-470 Phillips-Wangensteen Building Minneapolis Campus Sponsored by The Frederick James Bollum Endowed Research Fund for Biochemistry NIVERSITY OF INNESOTA _____________________________________________________________________________________________U M Twin Cities Campus Department of Biochemistry, 6-155 Jackson Hall Molecular Biology and Biophysics 321 Church St. SE Minneapolis, MN, 55455 Medical School and V: (612) 625-6100 College of Biological Sciences F: (612) 625-2163 http://www.cbs.umn.edu/bmbb May 14, 2015 Dear Friends; Welcome to the Centennial Celebration commemorating the 100th anniversary of the first PhD granted in biochemistry at the University of Minnesota. Morris J. Blish was our first PhD recipient and he went on to a marvelously distinguished career in the food industry and was recognized by the U of MN in 1952 by President Morrill with the Outstanding
    [Show full text]
  • Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes
    molecules Article Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes Piotr Minkiewicz * , Małgorzata Darewicz , Anna Iwaniak and Marta Turło Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszy´nski1, 10-726 Olsztyn-Kortowo, Poland; [email protected] (M.D.); [email protected] (A.I.); [email protected] (M.T.) * Correspondence: [email protected]; Tel.: +48-89-523-3715 Abstract: Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future. Keywords: amino acids; peptides; phosphorylation; phosphate groups; databases; code; bioinformatics; cheminformatics; SMILES Citation: Minkiewicz, P.; Darewicz, M.; Iwaniak, A.; Turło, M. Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using 1. Introduction Biological and Chemical Codes.
    [Show full text]
  • Metabolic Profiling Detects Biomarkers of Protein Degradation in COPD Patients
    Metabolic profiling detects biomarkers of protein degradation in COPD patients On‐line data supplement Baljit K. Ubhi, John H. Riley, Paul A. Shaw, David A. Lomas, Ruth Tal-Singer, William MacNee, Jules L Griffin, Susan C Connor Materials and Methods: ECLIPSE is a 3 year longitudinal study with samples collected at baseline, 3 and 6 months and then every 6 months for 3 years. Control subjects consisting of current or former smokers and individuals who have never smoked (n=566), were recruited as comparators with the COPD subjects (2756). The COPD patients were selected according to the following criteria; an forced expiratory volume in the first second (FEV1) of less than 80% of predicted normal and a baseline FEV1/ forced vital capacity(FVC) ratio of less than 0.7, aged 40-75 and either current or ex-smokers with a greater than 10 pack-year history. Patients were categorised according to the criteria from the Global Initiative for Chronic Obstructive Lung Disease (GOLD status; (E1)) i.e. COPD patients had an FEV1/FVC ratio of less than 70% and were subdivided into GOLD stage II, stage III and stage IV based on an 50%<FEV1<80%, 30%<FEV1<50% and <30% FEV1 predicted respectively. The control group consists of a cohort of 343 current and ex-smokers with greater than 10 pack-year smoking history and a second cohort of 223 who have never smoked (less than 1 pack-year smoking history). Both cohorts that make up the control groups have a baseline FEV1 greater than 85% predicted and a FEV1/FVC ratio of greater than 0.7.
    [Show full text]
  • Properties and Units in the Clinical Laboratory Sciences Part X
    Pure Appl. Chem., Vol. 72, No. 5, pp. 747–972, 2000. © 2000 IUPAC INTERNATIONAL FEDERATION OF CLINICAL CHEMISTRY AND LABORATORY MEDICINE SCIENTIFIC DIVISION COMMITTEE ON NOMENCLATURE, PROPERTIES AND UNITS (C-NPU)# and INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY CHEMISTRY AND HUMAN HEALTH DIVISION CLINICAL CHEMISTRY SECTION COMMISSION ON NOMENCLATURE, PROPERTIES AND UNITS (C-NPU)§ PROPERTIES AND UNITS IN THE CLINICAL LABORATORY SCIENCES PART X. PROPERTIES AND UNITS IN GENERAL CLINICAL CHEMISTRY (Technical Report) (IFCC–IUPAC 1999) Prepared for publication by HENRIK OLESEN1, INGE IBSEN1, IVAN BRUUNSHUUS1, DESMOND KENNY2, RENÉ DYBKÆR3, XAVIER FUENTES-ARDERIU4, GILBERT HILL5, PEDRO SOARES DE ARAUJO6, AND CLEM McDONALD7 1Office of Laboratory Informatics, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark; 2Dept. of Clinical Biochemistry, Our Lady’s Hospital for Sick Children, Dublin, Ireland; 3Dept. of Standardisation in Laboratory Medicine, Kommunehospitalet, Copenhagen, Denmark; 4Dept. of Clinical Biochemistry, Ciutat Sanitària i Universitària de Bellvitge, Barcelona, Spain; 5Dept. of Clinical Chemistry, Hospital for Sick Children, Toronto, Canada; 6Dept. of Biochemistry, IQUSP, São Paolo, Brazil; 7Regenstrief Inst. for Health Care, Indiana University School of Medicine, Indianapolis, Indiana, USA #§The combined Memberships of the Committee and the Commission (C-NPU) during the preparation of this report (1994 to 1996) were as follows: Chairman: H. Olesen (Denmark, 1989–1995); D. Kenny (Ireland, 1996). Members: X. Fuentes-Arderiu (Spain, 1991–1997); J. G. Hill (Canada; 1987–1997); D. Kenny (Ireland, 1994–1997); H. Olesen (Denmark, 1985–1995); P. L. Storring (UK, 1989–1995); P. Soares de Araujo (Brazil, 1994–1997); R. Dybkær (Denmark, 1996–1997); C. McDonald (USA, 1996–1997). Please forward comments to: H.
    [Show full text]