Supporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1

Size: px
Start display at page:

Download "Supporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1"

Transcription

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 University, 79 Freiburg, Germany April, 7 To whom correspondence should be addressed S

2 CIS TRANS FIG. S: Secondary structure content of PDZS in (top) cis and (bottom) trans state for the equilibrium MD simulations. The content of β-sheet (red), α-helical (blue) and -helical conformations of the individual residues are shown obtained by DSSP (W. Kabsch and C. Sander, Biopolymers, 77-7 (98)). S

3 S i S j i j P type α α Gln-7 Thr-77. HB mc α α Ala-7 Leu-78. HB mc α α Val-7 Arg-79. HB mc α α Val-7 Leu HB mc α β -β Cys-7 Ser-7 -. α β -β Leu-78 Lys- -. α β -β Leu-78 Leu np α β Val-7 Val- -. np α β Arg-79 Cys-. α β Ala-7 Ile-.7 np α β Leu-78 Ile-. np α β Thr-77 Val-. α β Leu-78 Val-8 -. np α β -α Gln-7 Ala-9. α β -α Ala-7 Ala-9. np α β -α Val-7 Leu- -. np α β -α Thr-77 Leu-. β -α β Gly-8 Ser-. HB sc β C Glu-9 Gln-9.8 β -β β -β Lys- Asp- -.8 β -β β -β Lys- Ser-7. β -β β -β Asn- Ser-7. HB mc β -β α -β Asn- Gln-8 -. β -β β -β Gly- Gly- -. β -β β -α His- Glu-7. β -β C Val- Ser-9.8 β -β C Val- Pro-9. β β -α Ile- Ala-9 -. np β β -α Ile- Thr β C Tyr- Ser-9. α -β C Gly- Gln-9. α -β C Gly- Ser-9. β β -α Arg-7 Glu-7. β α -β Val- Thr-8. TABLE S: Contacts between residue i in segment S i and residue j in segment S j that change significantly ( P ij.) upon cis-trans isomerization of PDZS, where P ij = Pij trans Pij cis denotes the change of the contact probability. Here Pij cis or Pij trans denote the probability that the minimal distance between residue i and j in PDZS-cis or -trans, respectively, is below. nm. The last column indicates whether a given contact is a H bond within the main chain (HB mc ), a H bond between the main and a side chain (HB sc ), or a contact between two hydrophobic residues (np). In line with the discussion, the upper part of the table describes contact changes at the α side and the lower part changes at the β side of the binding pocket. S

4 Residue rmsd(nm) Region cis trans d i,i+ (nm) s Gly-. N δ δ, P II, ɛ.(±.) Lys-. β, P II, ζ, δ P II.(±.) Asn-. P II, α, P II, (β) β, (P II, α).(±.) Asp-. β β α, β, γ, δ δ.(±.7) - Asn-. α, β, P II, δ, δ δ, α.77(±.) - Gly-9.9 δ, P II δ.9(±.) Gly-.7 β, P II, α, P II, ɛ, δ P II, (P II, ɛ).(±.) - Val-. β, P II, (α) β, P II, δ, (α).(±.) - Asn-7. P II, α, δ δ, (β, P II ).(±.) Thr-8. β β β, P II, α β, (P II, α, δ ).(±.) Ser-9. α, δ, (P II ) α, δ, P II.(±.8) Arg-. α, δ, (P II ) β, δ, α, γ.7(±.) Gly-.9 P II, ɛ, α, δ, P II P II, ɛ, α, δ, P II, (ɛ).8(±.) - Gly-. P II, P II, ɛ P II, P II, (ɛ).(±.7) - Lys-. α β P II, α P II, (α).(±.78) Leu-. α, (β) α.(±.8) - Glu-7. P II, α α, (P II ).(±.) - Gly-8. β α α, δ, γ α, δ, (γ).9(±.) - Ala-9. β, P II, (α) β, P II.(±.) Thr-7.7 P II, α, δ P II.(±.) His-7. α, (β, P II ) α.(±.7) Cys-7.98 α δ, α α.(±.) Asn-8.7 α, γ γ, (α, β).8(±.) - Gly-9. C P II, (P II ) P II, α, δ.(±.) - TABLE S: Residues i showing large changes in their main chain conformations between cis and trans state and extent of changes. The latter is quantified in terms of the rmsd between the average structures of the residues in the cis and trans state. Only residues with rmsd values above.8 nm are listed. Corresponding motifs in the cis and trans state are given in the nomenclature proposed by Hollingsworth and Karplus (Bioimol. Concepts, 7-8 ()). Brackets indicate motifs that are only weakly populated. In addition, changes in the C α distances between corresponding neigboring residues i and i+, d i,i+, are given. The rightmost column, s, indicates whether the changes are within the statistical error (s = ), or, if not, indicating that residue i is a hinge residue, it yields the sign of d i,i+. Thus, s < or s > means that the C α distance between residues i and i + is reduced or increased, respectively. S

5 residue x x x x x x x7 FIG. S: (Top) Influence of the 9 preselected dihedral angles on the first seven eigenvectors of dpca+ (see Methods section of main text). (Bottom) Distributions and time traces of the means and variances of principal components x x 7. S

6 FIG. S: Ramachandran plots of (top left) Asn in cis, (top right) Asn in trans, (bottom left) Ser 9 in cis, and (bottom right) Ser 9 in trans configuration. S

7 a b c d FIG. S: Ramacolor plots (F. Sittel and G. Stock, J. Chem. Theory Comp., - ()) for selected cis (b), NEQ (c), and trans (d) microstates. As displayed by the φ, ψ color space in (a), the plots give an impression of the structural differences of states and their respective secondary structure content. The x-axis gives the state while the y-axis denotes the index of a residue. The colors of the boxes are computed from the color code weighted by the intra state distribution in the Ramachandran plot. The typical secondary structure elements are highlighted by green (α-helix), red (β-sheet) and blue (left-handed α-helix). S7

8 State.8.. ca_dist_9_9 State.8.. ca_dist_9_9 State.8.. ca_dist_9_9 State.8.. ca_dist_9_ ca_dist ca_dist ca_dist ca_dist 7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.... contact_dist.... contact_dist.... contact_dist.... contact_dist contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist contact_dist contact_dist contact_dist contact_dist 9 FIG. S: Distance distributions (in units of nm) of selected microstates ( of ). S8

9 State ca_dist_9_9 State ca_dist_9_9 State ca_dist_9_9 State ca_dist_9_ ca_dist ca_dist ca_dist ca_dist 7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.... contact_dist.... contact_dist.... contact_dist.... contact_dist contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist contact_dist contact_dist contact_dist contact_dist 9 FIG. S: Distance distributions (in units of nm) of selected microstates ( of ). S9

10 # macrostates Qmin FIG. S: Number of macrostates as a function of the metastability Q min using a lag time of τ = ns. The macrostates are based on dynamical clustering using the Most Probable Path method by A. Jain and G. Stock (J. Chem. Theory Comp. 8, 8-89 ()). 8 7; 9 FIG. S7: Dynamical network of macrostates obtained for Q min =.7, placing the states according to their position in x -x space. Nodes are colored by their respective content of microstates identified as cis (blue), NEQ (green) or trans (red). Selected microstates are labeled at the macrostate they are part of. As in Fig. S, the macrostates and connections are based on dynamical clustering using the Most Probable Path method. S

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary

What 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 information

Physiochemical Properties of Residues

Physiochemical 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 information

Peptides And Proteins

Peptides 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 information

Secondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure

Secondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure Bioch/BIMS 503 Lecture 2 Structure and Function of Proteins August 28, 2008 Robert Nakamoto rkn3c@virginia.edu 2-0279 Secondary Structure Φ Ψ angles determine protein structure Φ Ψ angles are restricted

More information

Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27

Structure 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 information

Geometrical Concept-reduction in conformational space.and his Φ-ψ Map. G. N. Ramachandran

Geometrical Concept-reduction in conformational space.and his Φ-ψ Map. G. N. Ramachandran Geometrical Concept-reduction in conformational space.and his Φ-ψ Map G. N. Ramachandran Communication paths in trna-synthetase: Insights from protein structure networks and MD simulations Saraswathi Vishveshwara

More information

Ramachandran Plot. 4ysz Phi (degrees) Plot statistics

Ramachandran 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 information

Secondary and sidechain structures

Secondary 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 information

Proteins: Characteristics and Properties of Amino Acids

Proteins: Characteristics and Properties of Amino Acids SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.

More information

Packing of Secondary Structures

Packing 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 information

Properties of amino acids in proteins

Properties 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 information

Viewing and Analyzing Proteins, Ligands and their Complexes 2

Viewing 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 information

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 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 information

Protein structure. Protein structure. Amino acid residue. Cell communication channel. Bioinformatics Methods

Protein 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 information

C H E M I S T R Y N A T I O N A L Q U A L I F Y I N G E X A M I N A T I O N SOLUTIONS GUIDE

C H E M I S T R Y N A T I O N A L Q U A L I F Y I N G E X A M I N A T I O N SOLUTIONS GUIDE C H E M I S T R Y 2 0 0 0 A T I A L Q U A L I F Y I G E X A M I A T I SLUTIS GUIDE Answers are a guide only and do not represent a preferred method of solving problems. Section A 1B, 2A, 3C, 4C, 5D, 6D,

More information

Introduction to Comparative Protein Modeling. Chapter 4 Part I

Introduction 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 information

Supplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two

Supplementary 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 information

Protein Structures: Experiments and Modeling. Patrice Koehl

Protein 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 information

Model Mélange. Physical Models of Peptides and Proteins

Model 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 information

HSQC spectra for three proteins

HSQC 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 information

Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information

Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information Grzegorz Nawrocki and Marek Cieplak Institute of Physics, Polish Academy of Sciences,

More information

B O C 4 H 2 O O. NOTE: The reaction proceeds with a carbonium ion stabilized on the C 1 of sugar A.

B 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 information

Section Week 3. Junaid Malek, M.D.

Section 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 information

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease

NMR 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 information

Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination

Sequential 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 information

April, The energy functions include:

April, 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 information

Read more about Pauling and more scientists at: Profiles in Science, The National Library of Medicine, profiles.nlm.nih.gov

Read 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 information

Supersecondary Structures (structural motifs)

Supersecondary 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 information

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08

More information

Supporting Information

Supporting 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 information

Supplemental 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 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 information

Central Dogma. modifications genome transcriptome proteome

Central 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 information

Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate

Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate Stef Vanhaecht, Gregory Absillis, Tatjana N. Parac-Vogt* Department

More information

Structural and mechanistic insight into the substrate. binding from the conformational dynamics in apo. and substrate-bound DapE enzyme

Structural and mechanistic insight into the substrate. binding from the conformational dynamics in apo. and substrate-bound DapE enzyme Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 215 Structural and mechanistic insight into the substrate binding from the conformational

More information

Protein Structure Refinement Using 13 C α Chemical. Shift Tensors. Benjamin J. Wylie, Charles D. Schwieters, Eric Oldfield and Chad M.

Protein Structure Refinement Using 13 C α Chemical. Shift Tensors. Benjamin J. Wylie, Charles D. Schwieters, Eric Oldfield and Chad M. Protein Structure Refinement Using 13 C α Chemical Shift Tensors Benjamin J. Wylie, Charles D. Schwieters, Eric Oldfield and Chad M. Rienstra * Department of Chemistry, University of Illinois at Urbana-Champaign,

More information

Exam I Answer Key: Summer 2006, Semester C

Exam 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 information

Solutions In each case, the chirality center has the R configuration

Solutions 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 information

Supplementary 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 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 information

Supplementary Information Intrinsic Localized Modes in Proteins

Supplementary Information Intrinsic Localized Modes in Proteins Supplementary Information Intrinsic Localized Modes in Proteins Adrien Nicolaï 1,, Patrice Delarue and Patrick Senet, 1 Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute,

More information

Protein Fragment Search Program ver Overview: Contents:

Protein 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 information

Protein 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 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 information

7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?

7.012 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 information

Clustering and Model Integration under the Wasserstein Metric. Jia Li Department of Statistics Penn State University

Clustering and Model Integration under the Wasserstein Metric. Jia Li Department of Statistics Penn State University Clustering and Model Integration under the Wasserstein Metric Jia Li Department of Statistics Penn State University Clustering Data represented by vectors or pairwise distances. Methods Top- down approaches

More information

Resonance assignments in proteins. Christina Redfield

Resonance 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 information

What binds to Hb in addition to O 2?

What binds to Hb in addition to O 2? Reading: Ch5; 158-169, 162-166, 169-174 Problems: Ch5 (text); 3,7,8,10 Ch5 (study guide-facts); 1,2,3,4,5,8 Ch5 (study guide-apply); 2,3 Remember Today at 5:30 in CAS-522 is the second chance for the MB

More information

Other 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. 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 information

Any protein that can be labelled by both procedures must be a transmembrane protein.

Any 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 information

Journal of Pharmacology and Experimental Therapy-JPET#172536

Journal of Pharmacology and Experimental Therapy-JPET#172536 A NEW NON-PEPTIDIC INHIBITOR OF THE 14-3-3 DOCKING SITE INDUCES APOPTOTIC CELL DEATH IN CHRONIC MYELOID LEUKEMIA SENSITIVE OR RESISTANT TO IMATINIB Manuela Mancini, Valentina Corradi, Sara Petta, Enza

More information

Protein Structure Bioinformatics Introduction

Protein 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 information

Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell

Using 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 information

Supplementary 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 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 information

Dominant Paths in Protein Folding

Dominant Paths in Protein Folding Dominant Paths in Protein Folding Henri Orland SPhT, CEA-Saclay France work in collaboration with P. Faccioli, F. Pederiva, M. Sega University of Trento Henri Orland Annecy meeting 2006 Outline Basic notions

More information

Supplement information

Supplement information Electronic Supplementary Material (ESI) for Physil Chemistry Chemil Physics. This journal is the Owner Societies 216 Supplement information Fullerenol C 6 (OH) 16 prevents amyloid fibrillization of Aβ

More information

Exam III. Please read through each question carefully, and make sure you provide all of the requested information.

Exam III. Please read through each question carefully, and make sure you provide all of the requested information. 09-107 onors Chemistry ame Exam III Please read through each question carefully, and make sure you provide all of the requested information. 1. A series of octahedral metal compounds are made from 1 mol

More information

Overview. The peptide bond. Page 1

Overview. 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 information

Supporting Information. A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes

Supporting Information. A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes Supporting Information A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes Georgios Leonis, a Aggelos Avramopoulos, a Konstantinos D. Papavasileiou, a Heribert

More information

Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013

Protein 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 information

Computational Protein Design

Computational 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 information

Computer simulations of protein folding with a small number of distance restraints

Computer 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 information

Bacterial protease uses distinct thermodynamic signatures for substrate recognition

Bacterial protease uses distinct thermodynamic signatures for substrate recognition Bacterial protease uses distinct thermodynamic signatures for substrate recognition Gustavo Arruda Bezerra, Yuko Ohara-Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José A. Márquez,

More information

Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding

Folding 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 information

FW 1 CDR 1 FW 2 CDR 2

FW 1 CDR 1 FW 2 CDR 2 Supplementary Figure 1 Supplementary Figure 1: Interface of the E9:Fas structure. The two interfaces formed by V H and V L of E9 with Fas are shown in stereo. The Fas receptor is represented as a surface

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,

More information

Protein Secondary Structure Prediction using Feed-Forward Neural Network

Protein 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 information

Heteropolymer. Mostly in regular secondary structure

Heteropolymer. Mostly in regular secondary structure Heteropolymer - + + - Mostly in regular secondary structure 1 2 3 4 C >N trace how you go around the helix C >N C2 >N6 C1 >N5 What s the pattern? Ci>Ni+? 5 6 move around not quite 120 "#$%&'!()*(+2!3/'!4#5'!1/,#64!#6!,6!

More information

Basic Principles of Protein Structures

Basic 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 information

Supporting Information

Supporting Information Supporting Information Allosteric communication disrupted by small molecule binding to the Imidazole glycerol phosphate synthase protein-protein interface. Ivan Rivalta*,#, George P. Lisi #, Ning-Shiuan

More information

Course Notes: Topics in Computational. Structural Biology.

Course Notes: Topics in Computational. Structural Biology. Course Notes: Topics in Computational Structural Biology. Bruce R. Donald June, 2010 Copyright c 2012 Contents 11 Computational Protein Design 1 11.1 Introduction.........................................

More information

Unraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes

Unraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2015 Supporting Information for Unraveling the degradation of artificial amide bonds

More information

Full wwpdb X-ray Structure Validation Report i

Full wwpdb X-ray Structure Validation Report i Full wwpdb X-ray Structure Validation Report i Mar 14, 2018 02:00 pm GMT PDB ID : 3RRQ Title : Crystal structure of the extracellular domain of human PD-1 Authors : Lazar-Molnar, E.; Ramagopal, U.A.; Nathenson,

More information

Details of Protein Structure

Details 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 information

Peptide Syntheses. Illustrative Protection: BOC/ t Bu. A. Introduction. do not acid

Peptide Syntheses. Illustrative Protection: BOC/ t Bu. A. Introduction. do not acid Kevin Burgess, May 3, 2017 1 Peptide yntheses from chapter(s) in the recommended text A. Introduction do not acid -Met-e- -Met-Met- -e-e- -e-met- dipeptide dipeptide dipeptide dipeptide diketopiperazine

More information

Lecture 10: Brownian Motion, Random Walk & Diffusion Side Chains of Amino Acids

Lecture 10: Brownian Motion, Random Walk & Diffusion Side Chains of Amino Acids Lecture 10: Brownian Motion, Random Walk & Diffusion Side Chains of Amino Acids Lecturer: Prof. Brigita Urbanc (brigita@drexel.edu) PHYS 461 & 561, Fall 2009-2010 1 Stochastic Processes: Brownian Motion

More information

Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets

Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Supporting information Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Wan-Na Chen, Christoph Nitsche, Kala Bharath Pilla, Bim Graham, Thomas

More information

Chemistry Chapter 22

Chemistry 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 information

Oxygen Binding in Hemocyanin

Oxygen Binding in Hemocyanin Supporting Information for Quantum Mechanics/Molecular Mechanics Study of Oxygen Binding in Hemocyanin Toru Saito and Walter Thiel* Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470

More information

Bahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction

Bahnson 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 information

Translation. A ribosome, mrna, and trna.

Translation. 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 information

UNIT TWELVE. a, I _,o "' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I "-oh

UNIT TWELVE. a, I _,o ' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I -oh UNT TWELVE PROTENS : PEPTDE BONDNG AND POLYPEPTDES 12 CONCEPTS Many proteins are important in biological structure-for example, the keratin of hair, collagen of skin and leather, and fibroin of silk. Other

More information

Computer design of idealized -motifs

Computer design of idealized -motifs Computer design of idealized -motifs Andrzej Kolinski a) University of Warsaw, Department of Chemistry, Pasteura 1, 02-093 Warsaw, Poland and The Scripps Research Institute, Department of Molecular Biology,

More information

Bioinformatics Practical for Biochemists

Bioinformatics 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 information

Frequency Response of a Protein to Local Conformational Perturbations

Frequency Response of a Protein to Local Conformational Perturbations Frequency Response of a Protein to Local Conformational Perturbations Dilek Eren, Burak Alakent* Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey Abstract Signals created

More information

A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of

A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of Questions with Answers- Amino Acids & Peptides A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of 5.0-6.5 (Questions 1-4) 1. Which

More information

CHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D.

CHMI 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 information

Protein Structure. Role of (bio)informatics in drug discovery. Bioinformatics

Protein 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 information

BIOINF 4120 Bioinformatics 2 - Structures and Systems - Oliver Kohlbacher Summer Protein Structure Prediction I

BIOINF 4120 Bioinformatics 2 - Structures and Systems - Oliver Kohlbacher Summer Protein Structure Prediction I BIOINF 4120 Bioinformatics 2 - Structures and Systems - Oliver Kohlbacher Summer 2013 9. Protein Structure Prediction I Structure Prediction Overview Overview of problem variants Secondary structure prediction

More information

Supporting information

Supporting information Electronic Supplementary Material (ESI) for New Journal of Chemistry. This journal is The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2015 Supporting information Influence

More information

Molecular Structure Prediction by Global Optimization

Molecular 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 information

Statistically Based Reduced Representation of Amino Acid Side Chains

Statistically Based Reduced Representation of Amino Acid Side Chains J. Chem. Inf. Comput. Sci. 2004, 44, 817-830 817 Statistically Based Reduced Representation of Amino Acid Side Chains Jan K. Rainey and M. Cynthia Goh* Department of Chemistry, University of Toronto, Toronto,

More information

Protein Struktur (optional, flexible)

Protein 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 information

Diastereomeric resolution directed towards chirality. determination focussing on gas-phase energetics of coordinated. sodium dissociation

Diastereomeric resolution directed towards chirality. determination focussing on gas-phase energetics of coordinated. sodium dissociation Supplementary Information Diastereomeric resolution directed towards chirality determination focussing on gas-phase energetics of coordinated sodium dissociation Authors: samu Kanie*, Yuki Shioiri, Koji

More information

Supplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation

Supplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation Supplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation Javier L. Baylon, Ivan L. Lenov, Stephen G. Sligar and Emad Tajkhorshid

More information

7.012 Problem Set 1 Solutions

7.012 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 information

Advanced Certificate in Principles in Protein Structure. You will be given a start time with your exam instructions

Advanced 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 information

CHEM J-9 June 2014

CHEM J-9 June 2014 CEM1611 2014-J-9 June 2014 Alanine (ala) and lysine (lys) are two amino acids with the structures given below as Fischer projections. The pk a values of the conjugate acid forms of the different functional

More information

Supplementary information

Supplementary information Supplementary information The structural basis of modularity in ECF-type ABC transporters Guus B. Erkens 1,2, Ronnie P-A. Berntsson 1,2, Faizah Fulyani 1,2, Maria Majsnerowska 1,2, Andreja Vujičić-Žagar

More information

Protein 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 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 information

Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013

Ranjit 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 information

Electronic Supplementary Information

Electronic Supplementary Information Electronic Supplementary Information A Sensitive Phosphorescent Thiol Chemosensor Based on an Iridium(III) Complex with α,β-unsaturated Ketone Functionalized 2,2 -Bipyridyl Ligand Na Zhao, a Yu-Hui Wu,

More information

Full wwpdb X-ray Structure Validation Report i

Full wwpdb X-ray Structure Validation Report i Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 06:13 pm GMT PDB ID : 5G5C Title : Structure of the Pyrococcus furiosus Esterase Pf2001 with space group C2221 Authors : Varejao, N.; Reverter,

More information