Analysis of crystal structures

Slides:

Advertisements

Similar presentations

Determination of Protein Structure. Methods for Determining Structures X-ray crystallography – uses an X-ray diffraction pattern and electron density.

Advertisements

Intermolecular Forces. Intermolecular forces are weak, short-range attractive forces between atoms or molecules. Intermolecular forces ultimately derive.

Protein Primer. Outline n Protein representations n Structure of Proteins Structure of Proteins –Primary: amino acid sequence –Secondary:  -helices &

Class Notes: Chapter 6 sec.2. Polar Molecules Chemical bonding is the result of either an atom sharing one or more electrons with another atom or an atom.

How H 2 0 interacts with: Itself –Hydrogen-bonding Ions and charged functional groups –Solvation, screening, dielectric value Non-polar groups –The hydrophobic.

Introduction to Macromolecular X-ray Crystallography Biochem 300 Borden Lacy Print and online resources: Introduction to Macromolecular X-ray Crystallography,

 Four levels of protein structure  Linear  Sub-Structure  3D Structure  Complex Structure.

Homework 2 (due We, Feb. 1): Reading: Van Holde, Chapter 1 Van Holde Chapter 3.1 to 3.3 Van Holde Chapter 2 (we’ll go through Chapters 1 and 3 first. 1.Van.

Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop Robyn L. Stanfield, Jayant B. Ghiara, Erica O. Saphire, Albert T. Profy,

Chapter 4.1: Overview of Protein Structure CHEM 7784 Biochemistry Professor Bensley.

Atomic structure model

X-ray crystallography – an overview (based on Bernie Brown’s talk, Dept. of Chemistry, WFU) Protein is crystallized (sometimes low-gravity atmosphere is.

Chapter 10 Solids and Liquids. Intermolecular Forces These are considered to be “weak” forces… That is not to say that they do not serve an important.

Molecular mechanics Classical physics, treats atoms as spheres Calculations are rapid, even for large molecules Useful for studying conformations Cannot.

Structure Visualization

Introduction-2 Important molecular interactions in Biomolecules

PROTEINS LEVELS OF PROTEIN STRUCTURE Central Carbon Atom 3.

Organic Chemistry Lesson 21 X-ray crystallography.

Volume 92, Issue 5, Pages (March 2007)

Ultra-High Resolution X-ray Diffraction

Basic Chemistry and Water

High-Resolution Model of the Microtubule

Properties of Water freezing condensation melting cohesion

The Protonation State of the Glu-71/Asp-80 Residues in the KcsA Potassium Channel: A First-Principles QM/MM Molecular Dynamics Study Denis Bucher, Leonardo.

Ross Alexander Robinson, Xin Lu, Edith Yvonne Jones, Christian Siebold

The 1.85 Å Structure of Vaccinia Protein VP39: A Bifunctional Enzyme That Participates in the Modification of Both mRNA Ends Alec E Hodel, Paul D Gershon,

by Alexey Dementiev, Abel Silva, Calvin Yee, Zhe Li, Michael T

Molecular Dynamics Simulations on SDF-1α: Binding with CXCR4 Receptor

Volume 22, Issue 6, Pages (June 2014)

The Closing Mechanism of DNA Polymerase I at Atomic Resolution

Volume 25, Issue 5, Pages e3 (May 2017)

Crystal Structure at 2.8 Å of an FcRn/Heterodimeric Fc Complex

Volume 8, Issue 4, Pages (April 2001)

Liqun Zhang, Susmita Borthakur, Matthias Buck Biophysical Journal

How Does a Voltage Sensor Interact with a Lipid Bilayer

Ross Alexander Robinson, Xin Lu, Edith Yvonne Jones, Christian Siebold

Volume 3, Issue 2, Pages (February 1995)

Water 2:2 The single most abundant compound in most living things.

“DFG-Flip” in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop Harish Vashisth, Luca Maragliano, Cameron F.

Structure of the Cathelicidin Motif of Protegrin-3 Precursor

The Hydroxynitrile Lyase from Almond

Moosa Mohammadi, Joseph Schlessinger, Stevan R Hubbard Cell

Volume 25, Issue 5, Pages e3 (May 2017)

Volume 2, Issue 7, Pages (July 1994)

Volume 14, Issue 5, Pages (May 2006)

Volume 9, Issue 11, Pages (November 2001)

Volume 6, Issue 3, Pages (March 1998)

Volume 91, Issue 5, Pages (November 1997)

Crystal Structure of the Borna Disease Virus Nucleoprotein

Volume 10, Issue 6, Pages (June 2002)

Volume 106, Issue 10, Pages (May 2014)

Qun Liu, Qingqiu Huang, Xin Gen Lei, Quan Hao Structure

Volume 9, Issue 12, Pages (December 2001)

Volume 15, Issue 6, Pages (December 2001)

Volume 94, Issue 8, Pages (April 2008)

Refined structures of the active Ser83→Cys and impaired Ser46→Asp histidine- containing phosphocarrier proteins Der-Ing Liao, Osnat Herzberg Structure

Volume 18, Issue 9, Pages (September 2010)

Notes Page 27 of Unit Folder

Amedeo Caflisch, Martin Karplus Structure

Structure of a water soluble fragment of the ‘Rieske’ iron–sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing.

X-Ray Crystallography Reveals a Large Conformational Change during Guanyl Transfer by mRNA Capping Enzymes Kjell Håkansson, Aidan J. Doherty, Stewart.

Volume 87, Issue 7, Pages (December 1996)

OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme

Volume 11, Issue 1, Pages (January 2003)

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Mr.Halavath Ramesh 16-MCH-001 Dept. of Chemistry Loyola College University of Madras-Chennai.

Structural Basis for Ligand Recognition and Activation of RAGE

Tertiary structure of an immunoglobulin-like domain from the giant muscle protein titin: a new member of the I set Mark Pfuhl, Annalisa Pastore Structure

Presentation transcript:

Analysis of crystal structures Preconsiderations - Potential errors - Missing regions - Artifacts by crystal-packing - Resolutions Analysis of interactions - Hydrogen bonds - Hydrophobic interactions - Salt bridges - Surface charge representations Dynamics or flexibility - Temperature factor - Loop? Turn?

Electron density of crystal is average of all molecules in crystal Reality ideal Crystal Electron density

Potential errors in crystal structures Physical defects of crystals; damage of crystal in preparation, radiation damage during data collection Mosaicity of crystal Incompleteness of data Inaccuracy of high resolution data; vibration or rotation of side chains Result in bad electron density map

Physical defects of crystals Damages in preparation Melting Breaking into single crystal Uneven growth of crystal Radiation damage

Incompleteness and inaccuracy of diffraction data Blurred spot at high res. Loss of low res. data by beam stopper

Crystal packing artifact Different configuration of loop In solution In crystal

Resolution vs Rotamers of side chains > 3.5Å ~ 2.8Å

Crystallographic data collection and structure refinement statistics Rmeas (or Rsym); good as low I/sigma; background to intensity ratio, >2 or 3 R-work; <0.2 at <2.0A, ~0.25 at ~2.5A, <0.3 at >2.8 to 3.0A R-free; R-work + 0.05~0.07 is appropriate RMSD bond length; <0.01 RMSD bond angle; <1

Analysis of interactions Tools Visualization; Pymol, Coot Analysis; CCP4, VADAR

Analysis of interaction Hydrogen bonds 2.5 Å < distance between donor and acceptor < 3.5 Å 120° < angle N–O=C, etc., < 180° In protein to water, only distance matters Usually calculated by analysis program; ex.) VADAR

Analysis of interaction Hydrophobic interaction Non-real interaction; by exclusion of ordered water it increases net-entropy of system -> DG favorable As strong as hydrogen bonding when hydrocarbons are enough Shape complementary is a key to define (No distance or angle limit)

Analysis of interaction Salt bridge Electrostatic interaction between – (Glu, Asp) and + charged side chains (Lys, Arg) Distance; <5A Charge of each side chains must be head to head In <3A distance, they occasionally makes hydrogen bond

Analysis of interaction Surface charge representations Net surface charge distribution of protein Providing clue of binding sites in charge based interactions Positive charge – blue Negative charge - red

Flexibility of structure turn Scheme of turn Loop

Dynamics B-factor; temperature factor representing vibration of atom in temperature change