Secondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure
|
|
- Nora Gibson
- 5 years ago
- Views:
Transcription
1 Bioch/BIMS 503 Lecture 2 Structure and Function of Proteins August 28, 2008 Robert Nakamoto rkn3c@virginia.edu Secondary Structure Φ Ψ angles determine protein structure Φ Ψ angles are restricted by steric constraints The α-helix - regular local H-bond pattern The α-helix has a dipole moment Other helices β-strands - parallel and anti-parallel β-turns The statistics of α-helices and β-sheets - objective definitions of α-helices/β-sheets Prediction of transmembrane α-helices Further Reading Φ, Ψ angles alone determine protein structure Lehninger Biochemistry, Chapter 4, pp Matthews and van Holde (MvH) Biochemistry, Chapter 6, pp , Branden and Tooze (BT), Introduction to Protein Structure, Chapter 2, pp Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: Transmembrane Prediction Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: Figure 6.2: Rotation around the bonds in a polypeptide chain. 1
2 φ,ψ angles are restricted by steric constraints Figure 6.8: A Ramachandran plot. Figure 6.9: A sterically nonallowed conformation. Figure 6.2: Rotation around the bonds in a polypeptide chain. Figure 6.9: A sterically nonallowed conformation. Figure 6.3: The α helix and β sheet. Figure 6.4: Other possible secondary structures of polypeptides. Regular (repeating) structures in proteins 2
3 The α-helix Other helical structures: π and 3,10 The α-helix has a dipole moment Many α-helices are amphipathic (hydrophilic on one side, hydrophobic on the other) BT Fig. 2.3 Negatively charged groups (P0 4 ) frequently bind to the amino-ends of α helices. The dipole moment of an α helix, as well as possible H-bonds to free NH groups at the end, favors such binding. Different helical faces can have different properties BT Fig. 2.4 The helical wheel. Amino acid residues are plotted every 100 o around the wheel. Green: hydrophobic; Blue: polar; Red: charged. The second helix is amphipathic. Eisenberg s Hydrophobic moment ( ) 2 + ( H i cos("i) ) 2 µ H = # H i sin("i) i " =100 o for $ - helix " =180 o for % - strand # i polar - red hydrophobic - green 3
4 β strands and β sheets Parallel and anti-parallel β sheets BT Fig parallel β sheet BT Fig antiparallel β sheet Figure 6.18: Examples of β turns. β-turns Figure 6.19: A γ turn. 4
5 Figure 6.10: Ramachandran plot of the residues in bovine pancreatic trypsin inhibitor (BPTI). Currently 10,340 protein fold families in Pfam [ Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. Generally does not include membrane proteins. Goals of the Protein Structure Initiative - Structural Genomics Results of structural genomics Efficient Protein Target Selection Gene Cloning and Expression Protein Production Crystal Production and Delivery Structure Determination and Refinement Model Validation and Data Dissemination Structure-based functional assignment is still a challenge 5
6 Statistics of secondary structures Frequency of secondary structures W. Kabsch and C. Sander (1983) Biopolymers 22: W. Kabsch and C. Sander (1983) Biopolymers 22: Transmembrane secondary structures Glycophorin: an example transmembrane protein Note the predominance of hydrophobic amino acids within the bilayer. There is a huge energy penalty to place a charge in the low dielectric milieu of the bilayer. Charged residues are often in the form of ion pairs. Positive charged residues are often found at the cytoplasmic surface ( Positive Inside Rule ) BT Fig Aromatic residues are often found just inside the bilayer Glycosylation only occurs on the luminal or extracellular side 6
7 Examples of different topologies of membrane proteins: Topology of the HelB, HelC, and HelD proteins Difficulties in determination of membrane protein structure Usually very low expression levels Must remove the protein from its native environment, i.e., solubilization in detergents must identify the best detergent for solubility and stability Relatively low stability, especially in detergents Relatively highly dynamic with multiple conformations Relatively little surface exposure for crystal contacts From Goldman et al, Proc. Natl. Acad. Sci. USA, : Ca 2+ ATPase Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Toyoshima, C., Nomura, H. and Tsuda, T. (2004). Nature 432, Ion Channel Structure: the bacterial K + channel, KcsA 7
8 Porin Structure of porin refined at 1.8 Å resolution. Weiss MS, Schulz GE. J Mol Biol 1992, 227, ph Sensitive conformational change exposes the Influenza virus hemagglutinin fusion peptide The exposed fusion peptide inserts into the target membrane leading to membrane fusion Amino acid Hydropathicity/Hydrophobicity Hopp T.P., Woods K.R. (1981) PNAS. 78: Kyte J., Doolittle R.F. (1982). J. Mol. Biol. 157: D. M. Engelman, T. A. Steitz, A. Goldman, (1986) Annu. Rev. Biophys. Biophys. Chem. 15, 321 Hopp/ Woods Arg: Lys: Asp: Glu: Ser: Gln: Asn: Pro: Gly: Thr: His: Ala: Cys: Met: Val: Leu: Ile: Tyr: Phe: Trp: Kyte/ Doolittle Arg: Lys: Asp: Glu: Gln: Asn: His: Pro: Tyr: Trp: Ser: Thr: Gly: Ala: Met: Cys: Phe: Leu: Val: Ile: GES Arg: Asp: Lys: Glu: Asn: Gln: His: Tyr: Pro: Ser: Gly: Thr: Ala: Trp: Cys: Val: Leu: Ile: Met: Phe: Prediction of membrane topology based on hydropathy analysis
9 R K D B N S E H Z Q T G A P V Y C M I L W F X E V N N E S F V I Y M F V V H F T R K D B N S E H Z Q T G A P V Y C M I L W F E V N N E S F V I Y M F V V H F T R K D B N S E H Z Q T G A P V Y C M I L W F X E V N N E S F V I Y M F V V H F T
10 10
11 Secondary structure summary: Review questions The path of the Cα backbone (which determines the shape of the protein) is fully determined by the Φ and Ψ angles around each Cα Φ, Ψ values are strongly constrained by steric hindrance The two classes of repeating Φ,Ψ structures are helices (α, π, 3,10) and β strands (which make parallel and anti-parallel sheets) The interactions stabilizing α-helices and β-strands are backbone H-bonds (no role for side chain) α-helix H-bonds are local; β sheet interactions can be distant in sequence sequential β-strand side-chains face opposite directions Secondary structures in proteins are short; α-helices range from 4-20 amino acids (ave ~ 8-10); β-strands are shorter (ave ~ 4 amino acids) Transmembrane α-helices can be predicted from hydrophobicity 1. What is the direction of the α-helical dipole moment? 2. Why are δ=100 o and δ=180 o used to calculate Eisenberg s hydrophobic moment? 3. Order the following helical structures by helix diameter from smallest to largest? 4. Some proteins contain only β-strand secondary structure. What type of β-sheet must these strands form? 5. What is the minimum size of an α-helix? A β- strand? 6. What is the average size of an α-helix in a soluble protein? In a transmembrane domain? Questions from previous exams: 1. Describe the structural features exhibited by the polypeptide backbone of both types of beta-sheet. What is the effect of a single amino-acid insertion into a beta-strand? Why might one expect it to be more difficult to predict beta-strands than alpha-helices based on sequence information alone? Are beta-strands predicted less accurately? 2. Describe the structural features exhibited by the polypeptide backbone of an alpha-helix. Why does proline disrupt the regular pattern of an alpha-helix as proline is located in the middle of the helical segment, but has no disruptive effect when it is located at the N-terminus of the same helical segment? 3. Name two scales have been used for transmembrane helix prediction and describe how were they derived? Transmembrane helix prediction is very accurate; does this accuracy support the observation that most soluble proteins have a hydrophobic core? Why or why not? 4. Pick 5 amino acids, 2 hydrophobic, 2 charged, and 1 uncharged hydrophilic. (a) Name the 5 amino-acids, using their full name and either the standard 3-letter or 1-letter code. (b) Give each of the amino-acids an approximate hydropathy value, using a range of (c) write down a 10-amino-acid sequence using your 5 amino-acids and plot a Kyte-Doolittle hydropathy plot using a 3-amino-acid window for the 10-amino-acid sequence. 11
Major Types of Association of Proteins with Cell Membranes. From Alberts et al
Major Types of Association of Proteins with Cell Membranes From Alberts et al Proteins Are Polymers of Amino Acids Peptide Bond Formation Amino Acid central carbon atom to which are attached amino group
More informationPhysiochemical Properties of Residues
Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)
More informationOverview. The peptide bond. Page 1
Overview Secondary structure: the conformation of the peptide backbone The peptide bond, steric implications Steric hindrance and sterically allowed conformations. Ramachandran diagrams Side chain conformations
More informationSecondary and sidechain structures
Lecture 2 Secondary and sidechain structures James Chou BCMP201 Spring 2008 Images from Petsko & Ringe, Protein Structure and Function. Branden & Tooze, Introduction to Protein Structure. Richardson, J.
More informationAny protein that can be labelled by both procedures must be a transmembrane protein.
1. What kind of experimental evidence would indicate that a protein crosses from one side of the membrane to the other? Regions of polypeptide part exposed on the outside of the membrane can be probed
More informationIntroduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
More informationSequential resonance assignments in (small) proteins: homonuclear method 2º structure determination
Lecture 9 M230 Feigon Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination Reading resources v Roberts NMR of Macromolecules, Chap 4 by Christina Redfield
More informationPeptides And Proteins
Kevin Burgess, May 3, 2017 1 Peptides And Proteins from chapter(s) in the recommended text A. Introduction B. omenclature And Conventions by amide bonds. on the left, right. 2 -terminal C-terminal triglycine
More informationProtein Structure. Role of (bio)informatics in drug discovery. Bioinformatics
Bioinformatics Protein Structure Principles & Architecture Marjolein Thunnissen Dep. of Biochemistry & Structural Biology Lund University September 2011 Homology, pattern and 3D structure searches need
More informationPacking of Secondary Structures
7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding and Human Disease Professor Gossard Retrieving, Viewing Protein Structures from the Protein Data Base Helix helix packing Packing of Secondary
More informationProperties of amino acids in proteins
Properties of amino acids in proteins one of the primary roles of DNA (but not the only one!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated
More informationProtein structure. Protein structure. Amino acid residue. Cell communication channel. Bioinformatics Methods
Cell communication channel Bioinformatics Methods Iosif Vaisman Email: ivaisman@gmu.edu SEQUENCE STRUCTURE DNA Sequence Protein Sequence Protein Structure Protein structure ATGAAATTTGGAAACTTCCTTCTCACTTATCAGCCACCT...
More informationB O C 4 H 2 O O. NOTE: The reaction proceeds with a carbonium ion stabilized on the C 1 of sugar A.
hbcse 33 rd International Page 101 hemistry lympiad Preparatory 05/02/01 Problems d. In the hydrolysis of the glycosidic bond, the glycosidic bridge oxygen goes with 4 of the sugar B. n cleavage, 18 from
More informationWhat makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary
Electronic Supplementary Material (ESI) for Journal of Materials Chemistry B. This journal is The Royal Society of Chemistry 21 What makes a good graphene-binding peptide? Adsorption of amino acids and
More informationProblem Set 1
2006 7.012 Problem Set 1 Due before 5 PM on FRIDAY, September 15, 2006. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. For each of the following parts, pick
More informationProtein Structures: Experiments and Modeling. Patrice Koehl
Protein Structures: Experiments and Modeling Patrice Koehl Structural Bioinformatics: Proteins Proteins: Sources of Structure Information Proteins: Homology Modeling Proteins: Ab initio prediction Proteins:
More informationProtein Structure Bioinformatics Introduction
1 Swiss Institute of Bioinformatics Protein Structure Bioinformatics Introduction Basel, 27. September 2004 Torsten Schwede Biozentrum - Universität Basel Swiss Institute of Bioinformatics Klingelbergstr
More informationRead more about Pauling and more scientists at: Profiles in Science, The National Library of Medicine, profiles.nlm.nih.gov
2018 Biochemistry 110 California Institute of Technology Lecture 2: Principles of Protein Structure Linus Pauling (1901-1994) began his studies at Caltech in 1922 and was directed by Arthur Amos oyes to
More informationStructure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27
Acta Cryst. (2014). D70, doi:10.1107/s1399004714021695 Supporting information Volume 70 (2014) Supporting information for article: Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase
More informationThe Structure and Functions of Proteins
Wright State University CORE Scholar Computer Science and Engineering Faculty Publications Computer Science and Engineering 2003 The Structure and Functions of Proteins Dan E. Krane Wright State University
More informationSupersecondary Structures (structural motifs)
Supersecondary Structures (structural motifs) Various Sources Slide 1 Supersecondary Structures (Motifs) Supersecondary Structures (Motifs): : Combinations of secondary structures in specific geometric
More informationSupporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1
Supporting information to: Time-resolved observation of protein allosteric communication Sebastian Buchenberg, Florian Sittel and Gerhard Stock Biomolecular Dynamics, Institute of Physics, Albert Ludwigs
More informationModel Mélange. Physical Models of Peptides and Proteins
Model Mélange Physical Models of Peptides and Proteins In the Model Mélange activity, you will visit four different stations each featuring a variety of different physical models of peptides or proteins.
More informationProtein Structure. W. M. Grogan, Ph.D. OBJECTIVES
Protein Structure W. M. Grogan, Ph.D. OBJECTIVES 1. Describe the structure and characteristic properties of typical proteins. 2. List and describe the four levels of structure found in proteins. 3. Relate
More informationAdvanced Certificate in Principles in Protein Structure. You will be given a start time with your exam instructions
BIRKBECK COLLEGE (University of London) Advanced Certificate in Principles in Protein Structure MSc Structural Molecular Biology Date: Thursday, 1st September 2011 Time: 3 hours You will be given a start
More informationBIRKBECK COLLEGE (University of London)
BIRKBECK COLLEGE (University of London) SCHOOL OF BIOLOGICAL SCIENCES M.Sc. EXAMINATION FOR INTERNAL STUDENTS ON: Postgraduate Certificate in Principles of Protein Structure MSc Structural Molecular Biology
More informationProtein Structure Basics
Protein Structure Basics Presented by Alison Fraser, Christine Lee, Pradhuman Jhala, Corban Rivera Importance of Proteins Muscle structure depends on protein-protein interactions Transport across membranes
More informationSection Week 3. Junaid Malek, M.D.
Section Week 3 Junaid Malek, M.D. Biological Polymers DA 4 monomers (building blocks), limited structure (double-helix) RA 4 monomers, greater flexibility, multiple structures Proteins 20 Amino Acids,
More informationExam I Answer Key: Summer 2006, Semester C
1. Which of the following tripeptides would migrate most rapidly towards the negative electrode if electrophoresis is carried out at ph 3.0? a. gly-gly-gly b. glu-glu-asp c. lys-glu-lys d. val-asn-lys
More informationViewing and Analyzing Proteins, Ligands and their Complexes 2
2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing
More informationCentral Dogma. modifications genome transcriptome proteome
entral Dogma DA ma protein post-translational modifications genome transcriptome proteome 83 ierarchy of Protein Structure 20 Amino Acids There are 20 n possible sequences for a protein of n residues!
More informationUsing Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell
Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell Mathematics and Biochemistry University of Wisconsin - Madison 0 There Are Many Kinds Of Proteins The word protein comes
More informationOutline. Levels of Protein Structure. Primary (1 ) Structure. Lecture 6:Protein Architecture II: Secondary Structure or From peptides to proteins
Lecture 6:Protein Architecture II: Secondary Structure or From peptides to proteins Margaret Daugherty Fall 2003 Outline Four levels of structure are used to describe proteins; Alpha helices and beta sheets
More informationBiological Macromolecules
Introduction for Chem 493 Chemistry of Biological Macromolecules Dr. L. Luyt January 2008 Dr. L. Luyt Chem 493-2008 1 Biological macromolecules are the molecules of life allow for organization serve a
More information7.012 Problem Set 1 Solutions
ame TA Section 7.012 Problem Set 1 Solutions Your answers to this problem set must be inserted into the large wooden box on wheels outside 68120 by 4:30 PM, Thursday, September 15. Problem sets will not
More informationThe Structure of Enzymes!
The Structure of Enzymes Levels of Protein Structure 0 order amino acid composition Primary Secondary Motifs Tertiary Domains Quaternary ther sequence repeating structural patterns defined by torsion angles
More informationThe Structure of Enzymes!
The Structure of Enzymes Levels of Protein Structure 0 order amino acid composition Primary Secondary Motifs Tertiary Domains Quaternary ther sequence repeating structural patterns defined by torsion angles
More informationObjective: Students will be able identify peptide bonds in proteins and describe the overall reaction between amino acids that create peptide bonds.
Scott Seiple AP Biology Lesson Plan Lesson: Primary and Secondary Structure of Proteins Purpose:. To understand how amino acids can react to form peptides through peptide bonds.. Students will be able
More informationRamachandran Plot. 4ysz Phi (degrees) Plot statistics
B Ramachandran Plot ~b b 135 b ~b ~l l Psi (degrees) 5-5 a A ~a L - -135 SER HIS (F) 59 (G) SER (B) ~b b LYS ASP ASP 315 13 13 (A) (F) (B) LYS ALA ALA 315 173 (E) 173 (E)(A) ~p p ~b - -135 - -5 5 135 (degrees)
More informationProtein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version Document Published by the wwpdb
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.30 Document Published by the wwpdb This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/index/index.html.
More informationDetails of Protein Structure
Details of Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Anne Mølgaard, Kemisk Institut, Københavns Universitet Learning Objectives
More informationProteins: Characteristics and Properties of Amino Acids
SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.
More informationProtein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013
Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013 The presentation is based on the presentation by Professor Alexander Dikiy, which is given in the course compedium:
More informationNMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease
University of Wollongong Research Online Faculty of Science - Papers (Archive) Faculty of Science, Medicine and Health 2009 NMR study of complexes between low molecular mass inhibitors and the West Nile
More informationSupplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two
Supplementary Figure 1. Biopanningg and clone enrichment of Alphabody binders against human IL 23. Positive clones in i phage ELISA with optical density (OD) 3 times higher than background are shown for
More informationPROTEIN SECONDARY STRUCTURE PREDICTION: AN APPLICATION OF CHOU-FASMAN ALGORITHM IN A HYPOTHETICAL PROTEIN OF SARS VIRUS
Int. J. LifeSc. Bt & Pharm. Res. 2012 Kaladhar, 2012 Research Paper ISSN 2250-3137 www.ijlbpr.com Vol.1, Issue. 1, January 2012 2012 IJLBPR. All Rights Reserved PROTEIN SECONDARY STRUCTURE PREDICTION:
More informationChapter 4: Amino Acids
Chapter 4: Amino Acids All peptides and polypeptides are polymers of alpha-amino acids. lipid polysaccharide enzyme 1940s 1980s. Lipids membrane 1960s. Polysaccharide Are energy metabolites and many of
More informationFolding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding
Proc. Nat. Acad. Sci. USA Vol. 68, No. 9, pp. 2293-2297, September 1971 Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding PETER N. LEWS, FRANK A. MOMANY, AND HAROLD A. SCHERAGA*
More informationResonance assignments in proteins. Christina Redfield
Resonance assignments in proteins Christina Redfield 1. Introduction The assignment of resonances in the complex NMR spectrum of a protein is the first step in any study of protein structure, function
More informationThe Potassium Ion Channel: Rahmat Muhammad
The Potassium Ion Channel: 1952-1998 1998 Rahmat Muhammad Ions: Cell volume regulation Electrical impulse formation (e.g. sodium, potassium) Lipid membrane: the dielectric barrier Pro: compartmentalization
More informationProtein Structure. Hierarchy of Protein Structure. Tertiary structure. independently stable structural unit. includes disulfide bonds
Protein Structure Hierarchy of Protein Structure 2 3 Structural element Primary structure Secondary structure Super-secondary structure Domain Tertiary structure Quaternary structure Description amino
More informationBahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction
Name page 1 of 6 Bahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction Part I. The ion Ca 2+ can function as a 2 nd messenger. Pick a specific signal transduction pathway
More information1. What is an ångstrom unit, and why is it used to describe molecular structures?
1. What is an ångstrom unit, and why is it used to describe molecular structures? The ångstrom unit is a unit of distance suitable for measuring atomic scale objects. 1 ångstrom (Å) = 1 10-10 m. The diameter
More information7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?
ame 7.01 Problem Set 1 Section Question 1 a) What are the four major types of biological molecules discussed in lecture? Give one important function of each type of biological molecule in the cell? b)
More informationTHE UNIVERSITY OF MANITOBA. PAPER NO: _1_ LOCATION: 173 Robert Schultz Theatre PAGE NO: 1 of 5 DEPARTMENT & COURSE NO: CHEM / MBIO 2770 TIME: 1 HOUR
THE UNIVERSITY OF MANITOBA 1 November 1, 2016 Mid-Term EXAMINATION PAPER NO: _1_ LOCATION: 173 Robert Schultz Theatre PAGE NO: 1 of 5 DEPARTMENT & COURSE NO: CHEM / MBIO 2770 TIME: 1 HOUR EXAMINATION:
More informationBasic Principles of Protein Structures
Basic Principles of Protein Structures Proteins Proteins: The Molecule of Life Proteins: Building Blocks Proteins: Secondary Structures Proteins: Tertiary and Quartenary Structure Proteins: Geometry Proteins
More informationAnnouncements. Primary (1 ) Structure. Lecture 7 & 8: PROTEIN ARCHITECTURE IV: Tertiary and Quaternary Structure
Announcements TA Office Hours: Brian Eckenroth Monday 3-4 pm Thursday 11 am-12 pm Lecture 7 & 8: PROTEIN ARCHITECTURE IV: Tertiary and Quaternary Structure Margaret Daugherty Fall 2003 Homework II posted
More informationProtein Struktur (optional, flexible)
Protein Struktur (optional, flexible) 22/10/2009 [ 1 ] Andrew Torda, Wintersemester 2009 / 2010, AST nur für Informatiker, Mathematiker,.. 26 kt, 3 ov 2009 Proteins - who cares? 22/10/2009 [ 2 ] Most important
More informationOutline. Levels of Protein Structure. Primary (1 ) Structure. Lecture 6:Protein Architecture II: Secondary Structure or From peptides to proteins
Lecture 6:Protein Architecture II: Secondary Structure or From peptides to proteins Margaret Daugherty Fall 2004 Outline Four levels of structure are used to describe proteins; Alpha helices and beta sheets
More informationComputer simulations of protein folding with a small number of distance restraints
Vol. 49 No. 3/2002 683 692 QUARTERLY Computer simulations of protein folding with a small number of distance restraints Andrzej Sikorski 1, Andrzej Kolinski 1,2 and Jeffrey Skolnick 2 1 Department of Chemistry,
More informationALL LECTURES IN SB Introduction
1. Introduction 2. Molecular Architecture I 3. Molecular Architecture II 4. Molecular Simulation I 5. Molecular Simulation II 6. Bioinformatics I 7. Bioinformatics II 8. Prediction I 9. Prediction II ALL
More informationProtein Secondary Structure Prediction using Feed-Forward Neural Network
COPYRIGHT 2010 JCIT, ISSN 2078-5828 (PRINT), ISSN 2218-5224 (ONLINE), VOLUME 01, ISSUE 01, MANUSCRIPT CODE: 100713 Protein Secondary Structure Prediction using Feed-Forward Neural Network M. A. Mottalib,
More informationTranslation. A ribosome, mrna, and trna.
Translation The basic processes of translation are conserved among prokaryotes and eukaryotes. Prokaryotic Translation A ribosome, mrna, and trna. In the initiation of translation in prokaryotes, the Shine-Dalgarno
More informationBioinformatics Practical for Biochemists
Bioinformatics Practical for Biochemists Andrei Lupas, Birte Höcker, Steffen Schmidt WS 2013/14 03. Sequence Features Targeting proteins signal peptide targets proteins to the secretory pathway N-terminal
More informationLecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions: Van der Waals Interactions
More informationTamer Barakat. Razi Kittaneh. Mohammed Bio. Diala Abu-Hassan
14 Tamer Barakat Razi Kittaneh Mohammed Bio Diala Abu-Hassan Protein structure: We already know that when two amino acids bind, a dipeptide is formed which is considered to be an oligopeptide. When more
More informationSolutions In each case, the chirality center has the R configuration
CAPTER 25 669 Solutions 25.1. In each case, the chirality center has the R configuration. C C 2 2 C 3 C(C 3 ) 2 D-Alanine D-Valine 25.2. 2 2 S 2 d) 2 25.3. Pro,, Trp, Tyr, and is, Trp, Tyr, and is Arg,
More informationBCH 4053 Exam I Review Spring 2017
BCH 4053 SI - Spring 2017 Reed BCH 4053 Exam I Review Spring 2017 Chapter 1 1. Calculate G for the reaction A + A P + Q. Assume the following equilibrium concentrations: [A] = 20mM, [Q] = [P] = 40fM. Assume
More informationSupplementary Information. Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1
Supplementary Information Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1 Philip D. Mosier 1, Meng-Jung Chiang 2, Zhengshi Lin 2, Yamei Gao 2, Bashayer Althufairi
More informationCHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D.
CHMI 2227 EL Biochemistry I Test 1 26 January 2007 Prof : Eric R. Gauthier, Ph.D. Guidelines: 1) Duration: 55 min 2) 14 questions, on 7 pages. For 70 marks (5 marks per question). Worth 15 % of the final
More informationProtein Structure & Motifs
& Motifs Biochemistry 201 Molecular Biology January 12, 2000 Doug Brutlag Introduction Proteins are more flexible than nucleic acids in structure because of both the larger number of types of residues
More informationBiomolecules: lecture 10
Biomolecules: lecture 10 - understanding in detail how protein 3D structures form - realize that protein molecules are not static wire models but instead dynamic, where in principle every atom moves (yet
More informationChemistry Chapter 22
hemistry 2100 hapter 22 Proteins Proteins serve many functions, including the following. 1. Structure: ollagen and keratin are the chief constituents of skin, bone, hair, and nails. 2. atalysts: Virtually
More informationBiomolecules: lecture 9
Biomolecules: lecture 9 - understanding further why amino acids are the building block for proteins - understanding the chemical properties amino acids bring to proteins - realizing that many proteins
More informationProtein Fragment Search Program ver Overview: Contents:
Protein Fragment Search Program ver 1.1.1 Developed by: BioPhysics Laboratory, Faculty of Life and Environmental Science, Shimane University 1060 Nishikawatsu-cho, Matsue-shi, Shimane, 690-8504, Japan
More informationMolecular Structure Prediction by Global Optimization
Molecular Structure Prediction by Global Optimization K.A. DILL Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94118 A.T. PHILLIPS Computer Science
More informationFigure 1. Molecules geometries of 5021 and Each neutral group in CHARMM topology was grouped in dash circle.
Project I Chemistry 8021, Spring 2005/2/23 This document was turned in by a student as a homework paper. 1. Methods First, the cartesian coordinates of 5021 and 8021 molecules (Fig. 1) are generated, in
More informationConformational Geometry of Peptides and Proteins:
Conformational Geometry of Peptides and Proteins: Before discussing secondary structure, it is important to appreciate the conformational plasticity of proteins. Each residue in a polypeptide has three
More informationBiochemistry Quiz Review 1I. 1. Of the 20 standard amino acids, only is not optically active. The reason is that its side chain.
Biochemistry Quiz Review 1I A general note: Short answer questions are just that, short. Writing a paragraph filled with every term you can remember from class won t improve your answer just answer clearly,
More informationSupplemental Materials for. Structural Diversity of Protein Segments Follows a Power-law Distribution
Supplemental Materials for Structural Diversity of Protein Segments Follows a Power-law Distribution Yoshito SAWADA and Shinya HONDA* National Institute of Advanced Industrial Science and Technology (AIST),
More informationApril, The energy functions include:
REDUX A collection of Python scripts for torsion angle Monte Carlo protein molecular simulations and analysis The program is based on unified residue peptide model and is designed for more efficient exploration
More informationLecture 26: Polymers: DNA Packing and Protein folding 26.1 Problem Set 4 due today. Reading for Lectures 22 24: PKT Chapter 8 [ ].
Lecture 26: Polymers: DA Packing and Protein folding 26.1 Problem Set 4 due today. eading for Lectures 22 24: PKT hapter 8 DA Packing for Eukaryotes: The packing problem for the larger eukaryotic genomes
More informationPROTEIN ORIGAMI - A PROGRAM FOR THE CREATION OF 3D PAPER MODELS OF FOLDED PEPTIDES
PROTEIN ORIGAMI - A PROGRAM FOR THE CREATION OF 3D PAPER MODELS OF FOLDED PEPTIDES MANUAL Protein ORIGAMI is a browser-based web application that allows the user to create straightforward 3D paper models
More informationReview. Membrane proteins. Membrane transport
Quiz 1 For problem set 11 Q1, you need the equation for the average lateral distance transversed (s) of a molecule in the membrane with respect to the diffusion constant (D) and time (t). s = (4 D t) 1/2
More informationConformational Analysis
Conformational Analysis C01 3 C C 3 is the most stable by 0.9 kcal/mole C02 K eq = K 1-1 * K 2 = 0.45-1 * 0.048 = 0.11 C04 The intermediate in the reaction of 2 has an unfavorable syn-pentane interaction,
More informationRanjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013
Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA
More informationTHE UNIVERSITY OF MANITOBA. PAPER NO: 409 LOCATION: Fr. Kennedy Gold Gym PAGE NO: 1 of 6 DEPARTMENT & COURSE NO: CHEM 4630 TIME: 3 HOURS
PAPER NO: 409 LOCATION: Fr. Kennedy Gold Gym PAGE NO: 1 of 6 DEPARTMENT & COURSE NO: CHEM 4630 TIME: 3 HOURS EXAMINATION: Biochemistry of Proteins EXAMINER: J. O'Neil Section 1: You must answer all of
More informationComputational Protein Design
11 Computational Protein Design This chapter introduces the automated protein design and experimental validation of a novel designed sequence, as described in Dahiyat and Mayo [1]. 11.1 Introduction Given
More informationHSQC spectra for three proteins
HSQC spectra for three proteins SH3 domain from Abp1p Kinase domain from EphB2 apo Calmodulin What do the spectra tell you about the three proteins? HSQC spectra for three proteins Small protein Big protein
More informationLS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor
LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor Note: Adequate space is given for each answer. Questions that require a brief explanation should
More informationProtein Struktur. Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep. wake up at slide 39
Protein Struktur Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep wake up at slide 39 Andrew Torda, Wintersemester 2016/ 2017 Andrew Torda 17.10.2016 [ 1 ] Proteins - who cares?
More informationSupplementary figure 1. Comparison of unbound ogm-csf and ogm-csf as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine
Supplementary figure 1. Comparison of unbound and as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine GM-CSF (slate) with bound GM-CSF in the GIF:GM-CSF complex (GIF: green,
More information4 Proteins: Structure, Function, Folding W. H. Freeman and Company
4 Proteins: Structure, Function, Folding 2013 W. H. Freeman and Company CHAPTER 4 Proteins: Structure, Function, Folding Learning goals: Structure and properties of the peptide bond Structural hierarchy
More informationIntroduction to the Ribosome Overview of protein synthesis on the ribosome Prof. Anders Liljas
Introduction to the Ribosome Molecular Biophysics Lund University 1 A B C D E F G H I J Genome Protein aa1 aa2 aa3 aa4 aa5 aa6 aa7 aa10 aa9 aa8 aa11 aa12 aa13 a a 14 How is a polypeptide synthesized? 2
More informationA prevalent intraresidue hydrogen bond stabilizes proteins
Supplementary Information A prevalent intraresidue hydrogen bond stabilizes proteins Robert W. Newberry 1 & Ronald T. Raines 1,2 * 1 Department of Chemistry and 2 Department of Biochemistry, University
More informationOther Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4.
Other Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4. Field Desorption 5. MS MS techniques Matrix assisted
More informationFinal Chem 4511/6501 Spring 2011 May 5, 2011 b Name
Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of
More informationSupporting Information
Supporting Information Micelle-Triggered b-hairpin to a-helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA HØctor Zamora-Carreras, [a] Beatriz Maestro,
More informationComparison between Bacteriorhodopsin and Halorhodopsin. Halorhodopsin (HR) and Bacteriorhodopsin (BR) belong to a subfamily of
Comparison between Bacteriorhodopsin and Halorhodopsin Halorhodopsin (HR) and Bacteriorhodopsin (BR) belong to a subfamily of heptahelical membrane proteins, the archaeal rhodopsins. They are found in
More information12/6/12. Dr. Sanjeeva Srivastava IIT Bombay. Primary Structure. Secondary Structure. Tertiary Structure. Quaternary Structure.
Dr. anjeeva rivastava Primary tructure econdary tructure Tertiary tructure Quaternary tructure Amino acid residues α Helix Polypeptide chain Assembled subunits 2 1 Amino acid sequence determines 3-D structure
More information