A Single Outer Sphere Mutation Stabilizes apo- Mn Superoxide Dismutase by 35 C and. Disfavors Mn Binding.
|
|
- Hugo Poole
- 5 years ago
- Views:
Transcription
1 Supporting information for A Single Outer Sphere Mutation Stabilizes apo- Mn Superoxide Dismutase by 35 C and Disfavors Mn Binding. Anne-Frances Miller* and Ting Wang Department of Chemistry, University of Kentucky, Lexington Kentucky, 40506, United States S 1
2 Table S1. Melting temperatures and associated thermodynamic parameters. a WTholoMn 2+ SOD T m b C ΔH kj/mol ΔS J/mol K 67.4 ± ± ± ± ± ± ± ± ±700 WTapoMnSOD Q146EholoMnSOD Q146EapoMnSOD 87.9 ± ± ±100 a Thermodynamic parameters for each transition were extracted using the van't Hoff analysis provided in the CDpro software (JASCO). In brief: ΔG = ΔH -TΔS (eq. S1) and ΔG = -RT ln(k eq ) (eq. S2). Solving eq. 2 for ln(k eq ) we have ln(k eq ) = -ΔG /RT = -ΔH /RT +ΔS /R (eq. S3). This linear form of the van't Hoff equation can applied to DSC data that have been treated to account for the slope of the baseline before and after the transition being characterized. Once this has been done, each value of the ellipticity reveals the fraction of the sample that has undergone unfolding (f u ) and the fraction remaining in the folded form (f f, for the example of a transition that corresponds to unfolding). Thus each θ 222 vs. temperature point corresponds to a value of K eq = f u /f f and the temperature, T. A replot of ln(k eq ) vs. 1/T ideally conforms to a straight line for which the slope is -ΔH /R and the intercept is ΔS /R, yielding estimates of ΔH and ΔS which are valid only so long as they do not change significantly within the temperature range of the transition and applicable to that transition near its T m. S 2
3 For the WT, the enthalpies are comparable to published values of 430 kj/mol for interleukin-4, kj/mol for RNase A and 243 kj/mol for lysozyme, 2 although they are two-fold lower than values for WT-MnSOD determined calorimetrically. 3 The entropies of unfolding are also comparable to published values, of -790 J/mol K and -530 J/mol K for RNase A and lysozyme, respectively. For Q146E, our data indicate that the T m of 88 C describes apomn-protein whereas the event near 49 C pertains to Q146E-holoMnSOD. Q146E-apoMnSOD displays more than doubling of both the enthalpic stabilization of the folded state and the change in entropy associated with unfolding, compared to WT-apoMnSOD. Direct comparison with WT is complicated by the fact that these parameters apply at a much higher temperature, however the much larger ΔH in conjunction with the structurally conservative nature of the mutation 4 suggests that Glu at position 146 benefits from favourable electrostatic interactions with a nearby His in folded apomnsod, 5 given that charge is the major distinction between Glu and Gln in apomnsod. It is appealing to propose that a Glu - His + salt bridge forms in the mutant and that protonation of the participating His has the effect of diminishing the site's affinity for Mn 2+. Both the other two His could be protonated even in WT-apoMnSOD due to interactions with Asp167 and Glu170.B, respectively. Thus we speculate that mutation of Gln146 to Glu could cause protonation of the last neutral His ligand and thereby create a larger proton displacement barrier to metal ion acquisition. b Standard errors of individual fits averaged 0.6 C, with a maximum of 1.6 C. S 3
4 MnSOD Q146 FeSOD Q69 Figure S1. Ribbon diagram of one monomer of MnSOD showing that Gln146 comes from the C-terminal domain (yellow-red ribbon) whereas the analogous Gln69 of FeSOD derives from the N-terminal domain (violet blue - green). Ligand amino acids and the Tyr and Trp that hydrogen bond with the active site Gln are shown as sticks. The active site Mn ion is a purple sphere and two water molecules in the coordination sphere at cryogenic temperature are provided as red dots. Figure is based on 1D5N.pdb and generated using Chimera. 6 S 4
5 Figure S2. Comparison of circular dichroism signatures of the secondary structure of WT-holoMn-SOD, WT-apoMnSOD and Q146E-apoMnSOD. Neither the Q146E mutation nor Mn binding significantly affects the secondary structure content of MnSOD, based on far-uv CD. S 5
6 20$ 30$ 40$ 50$ 60$ 70$ 80$ 90$ 100$!6000$ Temperature#( C)#!8000$!10000$!12000$!14000$!16000$!18000$!20000$!22000$ θ 222 #(deg cm 2 dmol -1 )# Figure S3. Comparison of CD melts of samples dominated by WT-Mn 2+ SOD vs. WT- reconstituted_wtholomnsod as-isolated_wtholomnsod Mn 3+ SOD. Samples were WT-MnrecSOD (prepared by Mn removal followed by reconstitution with Mn 2+, 0.95 ±.05 Mn/site) or WT-holoMnSOD as-isolated (1.0 ± 0.1 Mn/site). 15 μm SOD (dimers) were equilibrated in 5 mm potassium phosphate buffer at ph 7.4 with 0.8 M GdmCl to prevent protein aggregation, and the temperature was increased from 20 to 100 at 1 /min. At each temperature point (5 C intervals) four spectra were collected and the average value of θ 222 was recorded. Although our apparatus did not permit control of the oxidation state of the Mn ion over the course of the experiments, as-isolated WT-holoMnSOD (substantially Mn 3+ ) displayed a sharp transition above 80 C near the reported calorimetric T m of 90 C whereas freshly-reconstituted WT-holoMnSOD (containing more Mn 2+ ) displayed greater change in θ 222 near the calorimetric T m of 69 C and samples resulting from other S 6
7 treatments or storage displayed results in between. Thus redox heterogeneity provides an explanation for the broad and somewhat variable shapes of the high-temperature portions of the WT-holoMnSOD melting curves, as well as the range of values produced for T m by simple two-state fits. S 7
8 Figure S4. High resolution thermal melts monitored via θ 222. Samples were WTapoMnSOD (prepared by Mn removal from WT-holoMnSOD as per the methods (0.01 ±.01 Mn/site), WT-MnrecSOD (prepared by Mn removal followed by reconstitution with Mn, 0.95 ±.05 Mn/site) or Q146E-apoMnSOD prepared by denaturation followed by reconstitution with Mn (0.13 ±.01 Mn/site). 15 μm SOD (dimers) were equilibrated in 5 mm potassium phosphate buffer at ph 7.4 with 0.8 M GdmCl to prevent protein aggregation, and the temperature was increased from 20 to 100 at 1 /min, θ 222 was measured with a time constant of 1 s at 1 C intervals. The thermodynamic parameters describing protein thermal denaturation assuming a two-state process N U were extracted using the van t Hoff analysis method provided by CDpro (Jasco Co) and are reported in Table S1, above. WT- apomnsod WT- holomnsod Q146E-.1Mn/site S 8
9 Temperature)( C))!7000% 20%!9000% 30% 40% 50% 60% 70% 80% 90% 100%!11000% Ellip%city)Θ 222 )(deg cm 2 dmo l31 ))!13000%!15000%!17000%!19000%!21000%!23000%!25000%!27000% 0.1 Mn/site 0.01Mn/site <0.005 Mn/site Figure S5. Comparison of melts of Q146E-MnrecSOD vs. Q146-apoMnSOD using absolute vertical scale. Temperature-induced unfolding was compared among samples of Q146E-MnSOD containing Mn in different fractions of the active sites. Samples were Q146E-apoMnSOD as-isolated ( 0.02 Mn/site, 0.03 Mn/site) and Q146E-apoMnSOD prepared by denaturation followed by reconstitution with Mn (0.13 ±.01 Mn/site). Samples contained 15 μm of Q146E-SOD (dimers) in 5 mm potassium phosphate buffer at ph 7.4 with 0.8 M GdmCl to prevent protein aggregation, and the temperature was increased from 20 to 100 at 1 /min. For data collected every 5 degrees, four spectra were collected and averaged at each temperature. For data collected every one degrees, θ 222 was measured with a time constant of 1 s. S 9
10 REFERENCES [1] Vaz, D. C., Rodrigues, J. R., Sebald, W., Dobson, C. M., and Brito, R. M. M. (2006) Enthalpic and entropic contributions mediate the role of disulfide bonds on the conformational stability of interleuking-4., Prot. Sci. 15, [2] Makhatadze, G. I., and Privalov, P. L. (1995) Energetics of protein structure., Adv. Protein Chem 47, [3] Mizuno, K., Whittaker, M. M., Bachinger, H. P., and Whittaker, J. W. (2004) Calorimetric studies on the tight-binding metal interactions of Escherichia coli manganese superoxide dismutase., J. Biol. Chem. 279, [4] Yikilmaz, E., Rodgers, D. W., and Miller, A.-F. (2006) The crucial importance of chemistry in the structure-function link: Manipulating hydrogen bonding in ironcontaining superoxide dismutase., Biochemistry 45, [5] Whittaker, J. W., Lerch, T. F., Kirillova, O., Chapman, M. S., and Whittaker, J. W. (2011) Subunit dissociation and metal binding by Escherichi coli apo-manganese superoxide dismutase., Arch. Biochem. Biophys. 505, [6] Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera - a visualization system for exploratory research and analysis., J. Comput. Chem. 25, S 10
Other Cells. Hormones. Viruses. Toxins. Cell. Bacteria
Other Cells Hormones Viruses Toxins Cell Bacteria ΔH < 0 reaction is exothermic, tells us nothing about the spontaneity of the reaction Δ H > 0 reaction is endothermic, tells us nothing about the spontaneity
More informationBiology Chemistry & Physics of Biomolecules. Examination #1. Proteins Module. September 29, Answer Key
Biology 5357 Chemistry & Physics of Biomolecules Examination #1 Proteins Module September 29, 2017 Answer Key Question 1 (A) (5 points) Structure (b) is more common, as it contains the shorter connection
More information= (-22) = +2kJ /mol
Lecture 8: Thermodynamics & Protein Stability Assigned reading in Campbell: Chapter 4.4-4.6 Key Terms: DG = -RT lnk eq = DH - TDS Transition Curve, Melting Curve, Tm DH calculation DS calculation van der
More informationMicrocalorimetry for the Life Sciences
Microcalorimetry for the Life Sciences Why Microcalorimetry? Microcalorimetry is universal detector Heat is generated or absorbed in every chemical process In-solution No molecular weight limitations Label-free
More informationSupplementary Figures
1 Supplementary Figures Supplementary Figure 1 Type I FGFR1 inhibitors (a) Chemical structures of a pyrazolylaminopyrimidine inhibitor (henceforth referred to as PAPI; PDB-code of the FGFR1-PAPI complex:
More informationBiological Thermodynamics
Biological Thermodynamics Classical thermodynamics is the only physical theory of universal content concerning which I am convinced that, within the framework of applicability of its basic contents, will
More informationBCHS 6229 Protein Structure and Function. Lecture 3 (October 18, 2011) Protein Folding: Forces, Mechanisms & Characterization
BCHS 6229 Protein Structure and Function Lecture 3 (October 18, 2011) Protein Folding: Forces, Mechanisms & Characterization 1 The folding problem One of the greatest unsolved problems of Science The folding
More informationProtein folding. Today s Outline
Protein folding Today s Outline Review of previous sessions Thermodynamics of folding and unfolding Determinants of folding Techniques for measuring folding The folding process The folding problem: Prediction
More informationFull file at https://fratstock.eu
Chapter 03 1. a. DG=DH-TDS Δ G = 80 kj ( 98 K) 0.790 kj = 44.6 kj K b. ΔG = 0 @ T m. Unfolding will be favorable at temperatures above the T m. Δ G =Δ H TΔ S 0 kj kj 80 ( xk) 0.790 K 0 Δ G = = 354.4 K
More informationFree Energy. because H is negative doesn't mean that G will be negative and just because S is positive doesn't mean that G will be negative.
Biochemistry 462a Bioenergetics Reading - Lehninger Principles, Chapter 14, pp. 485-512 Practice problems - Chapter 14: 2-8, 10, 12, 13; Physical Chemistry extra problems, free energy problems Free Energy
More informationTable 1. Kinetic data obtained from SPR analysis of domain 11 mutants interacting with IGF-II. Kinetic parameters K D 1.
Kinetics and Thermodynamics of the Insulin-like Growth Factor II (IGF-II) Interaction with IGF-II/Mannose 6-phosphate Receptor and the function of CD and AB Loop Solvent-exposed Residues. Research Team:
More informationSupplementary Information
1 Supplementary Information Figure S1 The V=0.5 Harker section of an anomalous difference Patterson map calculated using diffraction data from the NNQQNY crystal at 1.3 Å resolution. The position of the
More informationMacromolecule Stability Curves
Chem728 page 1 Spring 2012 Macromolecule Stability Curves Macromolecule Transitions - We have discussed in class the factors that determine the spontaneity of processes using conformational transitions
More informationDSC Characterization of the Structure/Function Relationship for Proteins
DSC Characterization of the Structure/Function Relationship for Proteins Differential Scanning Calorimetry (DSC) DSC is recognized as Gold Std technique for measuring molecular thermal stability and structure
More information1. Use the Data for RNAse to estimate:
Chem 78 - - Spr 1 03/14/01 Assignment 4 - Answers Thermodynamic Analysis of RNAseA Denaturation by UV- Vis Difference Absorption Spectroscopy (and Differential Scanning Calorimetry). The accompanying excel
More informationL. METALS IN REDOX CATALYSIS
Metals in Redox Reactions L. METALS IN REDOX CATALYSIS While metals can assist a lot of important chemistry without themselves acting as reactants, they are uniquely able to serve a direct role in oxidation
More informationCarbohydrate- Protein interac;ons are Cri;cal in Life and Death. Other Cells. Hormones. Viruses. Toxins. Cell. Bacteria
ther Cells Carbohydrate- Protein interac;ons are Cri;cal in Life and Death ormones Viruses Toxins Cell Bacteria ow to Model Protein- ligand interac;ons? Protein Protein Protein DNA/RNA Protein Carbohydrate
More informationSolutions and Non-Covalent Binding Forces
Chapter 3 Solutions and Non-Covalent Binding Forces 3.1 Solvent and solution properties Molecules stick together using the following forces: dipole-dipole, dipole-induced dipole, hydrogen bond, van der
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
More informationSUPPLEMENTARY INFORMATION
Figure S1. Secondary structure of CAP (in the camp 2 -bound state) 10. α-helices are shown as cylinders and β- strands as arrows. Labeling of secondary structure is indicated. CDB, DBD and the hinge are
More informationCholera Toxin Invasion
Protein-carbohydrate interactions: Isothermal Titration Calorimetry Dr Bruce Turnbull School of Chemistry and Astbury Centre for Structural Molecular Biology University of Leeds Cholera Toxin Invasion
More informationCombined Isothermal Titration and Differential Scanning Calorimetry Define. Three-State Thermodynamics of fals-associated Mutant Apo SOD1 Dimers
Supporting Information for: Combined Isothermal Titration and Differential Scanning Calorimetry Define Three-State Thermodynamics of fals-associated Mutant Apo SOD1 Dimers and an Increased Population of
More informationProteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability
Proteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability Dr. Andrew Lee UNC School of Pharmacy (Div. Chemical Biology and Medicinal Chemistry) UNC Med
More informationSupporting Information
Supporting Information Boehr et al. 10.1073/pnas.0914163107 SI Text Materials and Methods. R 2 relaxation dispersion experiments. 15 NR 2 relaxation dispersion data measured at 1 H Larmor frequencies of
More informationThermodynamics. Entropy and its Applications. Lecture 11. NC State University
Thermodynamics Entropy and its Applications Lecture 11 NC State University System and surroundings Up to this point we have considered the system, but we have not concerned ourselves with the relationship
More informationLecture 2: Biological Thermodynamics [PDF] Key Concepts
Lecture 2: Biological Thermodynamics [PDF] Reading: Berg, Tymoczko & Stryer: pp. 11-14; pp. 208-210 problems in textbook: chapter 1, pp. 23-24, #4; and thermodynamics practice problems [PDF] Updated on:
More informationPaul Sigler et al, 1998.
Biological systems are necessarily metastable. They are created, modulated, and destroyed according to a temporal plan that meets the survival needs of the cell, organism, and species...clearly, no biological
More informationThermodynamics of Borax Dissolution
Thermodynamics of Borax Dissolution Introduction In this experiment, you will determine the values of H, G and S for the reaction which occurs when borax (sodium tetraborate octahydrate) dissolves in water.
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 informationAwanish Kumar, Anjeeta Rani and Pannuru Venkatesu* Department of Chemistry, University of Delhi, Delhi
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 2014 Supplimentary Informations
More informationBIOCHEMISTRY. František Vácha. JKU, Linz.
BIOCHEMISTRY František Vácha http://www.prf.jcu.cz/~vacha/ JKU, Linz Recommended reading: D.L. Nelson, M.M. Cox Lehninger Principles of Biochemistry D.J. Voet, J.G. Voet, C.W. Pratt Principles of Biochemistry
More informationBiotechnology of Proteins. The Source of Stability in Proteins (III) Fall 2015
Biotechnology of Proteins The Source of Stability in Proteins (III) Fall 2015 Conformational Entropy of Unfolding It is The factor that makes the greatest contribution to stabilization of the unfolded
More informationMCB100A/Chem130 MidTerm Exam 2 April 4, 2013
MCBA/Chem Miderm Exam 2 April 4, 2 Name Student ID rue/false (2 points each).. he Boltzmann constant, k b sets the energy scale for observing energy microstates 2. Atoms with favorable electronic configurations
More informationExp.3 Determination of the Thermodynamic functions for the Borax Solution
Exp.3 Determination of the Thermodynamic functions for the Borax Solution Theory: The relationship between Gibb s energy (ΔG), Enthalpy (ΔH), Entropy (ΔS) and the equilibrium constant (K) for a chemical
More informationMicrocalorimetric techniques
Microcalorimetric techniques Isothermal titration calorimetry (ITC) Differential scanning calorimetry (DSC) Filip Šupljika Filip.Supljika@irb.hr Laboratory for the study of interactions of biomacromolecules
More informationApplications of Free Energy. NC State University
Chemistry 433 Lecture 15 Applications of Free Energy NC State University Thermodynamics of glycolysis Reaction kj/mol D-glucose + ATP D-glucose-6-phosphate + ADP ΔG o = -16.7 D-glucose-6-phosphate p D-fructose-6-phosphate
More informationSUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Supplementary Figure 1 Protein sequence alignment of Vibrionaceae with either a 40-residue insertion or a 44-residue insertion. Identical residues are indicated by red background.
More informationProtein Folding experiments and theory
Protein Folding experiments and theory 1, 2,and 3 Protein Structure Fig. 3-16 from Lehninger Biochemistry, 4 th ed. The 3D structure is not encoded at the single aa level Hydrogen Bonding Shared H atom
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 informationChapter 1. Topic: Overview of basic principles
Chapter 1 Topic: Overview of basic principles Four major themes of biochemistry I. What are living organism made from? II. How do organism acquire and use energy? III. How does an organism maintain its
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 informationThermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy Two-state model versus sequential unfolding
REVIEW Thermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy Two-state model versus sequential unfolding Joachim Seelig 1 * and Hans-Joachim Schönfeld 2 1 Division
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 informationOCR Chemistry A H432
All the energy changes we have considered so far have been in terms of enthalpy, and we have been able to predict whether a reaction is likely to occur on the basis of the enthalpy change associated with
More information( 1 vρ) = ( sec)( N sec m 1 )
Page 1 of 5 + formula sheet 1. You have isolated a novel protein that has been implicated in a disease and you would like to use what you have learned in Chem/Biochem 471 to deduce some of its properties.
More informationEffect of the Single and Double Chain Surfactant Cobalt(III) Complexes on Their Hydrophobicity, Micelle Formation,
Electronic Supplementary Material (ESI) for Inorganic Chemistry Frontiers. This journal is the Partner Organisations 2014 Supplementary Information Effect of the Single and Double Chain Surfactant Cobalt(III)
More informationarxiv:cond-mat/ v1 7 Jul 2000
A protein model exhibiting three folding transitions Audun Bakk Department of Physics, Norwegian University of Science and Technology, NTNU, N-7491 Trondheim, Norway arxiv:cond-mat/0007130v1 7 Jul 2000
More informationCharacterizing Binding Interactions by ITC
Characterizing Binding Interactions by ITC Christin T. Choma TA Instruments, 19 Lukens Drive, New Castle, DE 1972, USA All biochemical reactions involve recognition, binding and the formation of noncovalent
More informationWhy Proteins Fold. How Proteins Fold? e - ΔG/kT. Protein Folding, Nonbonding Forces, and Free Energy
Why Proteins Fold Proteins are the action superheroes of the body. As enzymes, they make reactions go a million times faster. As versatile transport vehicles, they carry oxygen and antibodies to fight
More informationLecture 14 (10/18/17) Lecture 14 (10/18/17)
Lecture 14 (10/18/17) Reading: Ch6; 190-191, 194-195, 197-198 Problems: Ch6 (text); 7, 24 Ch6 (study guide-facts); 4, 13 NEXT Reading: Ch6; 198-203 Ch6; Box 6-1 Problems: Ch6 (text); 8, 9, 10, 11, 12,
More informationMCB100A/Chem130 MidTerm Exam 2 April 4, 2013
MCB1A/Chem13 MidTerm Exam 2 April 4, 213 Name Student ID True/False (2 points each). 1. The Boltzmann constant, k b T sets the energy scale for observing energy microstates 2. Atoms with favorable electronic
More informationHydrophobicity-Induced Prestaining for Protein Detection in Polyacrylamide
Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2016 Hydrophobicity-Induced Prestaining for Protein Detection in Polyacrylamide Gel Electrophoresis
More information3. Solutions W = N!/(N A!N B!) (3.1) Using Stirling s approximation ln(n!) = NlnN N: ΔS mix = k (N A lnn + N B lnn N A lnn A N B lnn B ) (3.
3. Solutions Many biological processes occur between molecules in aqueous solution. In addition, many protein and nucleic acid molecules adopt three-dimensional structure ( fold ) in aqueous solution.
More informationThermodynamic Stability of Hoogsteen and Watson-Crick. Base Pairs in the Presence of Histone H3-Mimicking Peptide
Supporting information Thermodynamic Stability of Hoogsteen and Watson-Crick Base Pairs in the Presence of Histone H3-Mimicking Peptide Smritimoy Pramanik a, Kaori Nakamura a, Kenji Usui a,b, Shu-ichi
More informationCHEM 3653 Exam # 1 (03/07/13)
1. Using phylogeny all living organisms can be divided into the following domains: A. Bacteria, Eukarya, and Vertebrate B. Archaea and Eukarya C. Bacteria, Eukarya, and Archaea D. Eukarya and Bacteria
More informationProton Acidity. (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: HA + K + B -
Proton Acidity A01 Given that acid A has a pk a of 15 and acid B has a pk a of 10, then: (a) Which of the two acids is stronger? (b) For the following reaction, draw the arrowhead properly to indicate
More informationS2004 Methods for characterization of biomolecular interactions - classical versus modern
S2004 Methods for characterization of biomolecular interactions - classical versus modern Isothermal Titration Calorimetry (ITC) Eva Dubská email: eva.dubska@ceitec.cz Outline Calorimetry - history + a
More information1 What is energy?
http://www.intothecool.com/ 1 What is energy? the capacity to do work? (Greek: en-, in; + ergon, work) the capacity to cause change to produce an effect? a certain quantity that does not change in the
More informationLABORATORY OF ELEMENTARY BIOPHYSICS. Isothermal Titration Calorimetry as a tool for determining thermodynamic parameters of chemical reactions
LABORATORY OF ELEMENTARY BIOPHYSICS Experimental exercises for III year of the First cycle studies Field: Applications of physics in biology and medicine Specialization: Molecular Biophysics Isothermal
More informationFST 123 Problem Set 3 Spring, V o at [S] 0 = 10 mm (mm/min)
FST 23 Problem Set 3 Spring, 2009 Name. A student needed to know the activity versus ph profile for an enzyme that he was going to use in a later application. He collected the appropriate data and determined
More informationLattice protein models
Lattice protein models Marc R. Roussel epartment of Chemistry and Biochemistry University of Lethbridge March 5, 2009 1 Model and assumptions The ideas developed in the last few lectures can be applied
More informationWhat 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 information7/19/2011. Models of Solution. State of Equilibrium. State of Equilibrium Chemical Reaction
Models of Solution Chemistry- I State of Equilibrium A covered cup of coffee will not be colder than or warmer than the room temperature Heat is defined as a form of energy that flows from a high temperature
More informationSubstrate-dependent switching of the allosteric binding mechanism of a dimeric enzyme
Supplementary Information: Substrate-dependent switching of the allosteric binding mechanism of a dimeric enzyme Lee Freiburger, 1 Teresa Miletti, 1 Siqi Zhu, 1 Oliver Baettig, Albert Berghuis, Karine
More informationIsothermal titration calorimetry (ITC)
Isothermal titration calorimetry (ITC) Peter.gimeson@malvern.com Why microcalorimetry? Label-free Broad dynamic range Information rich Ease-of-use Direct measurement of heat change (ITC) Direct measurement
More informationSupplementary Information. Overlap between folding and functional energy landscapes for. adenylate kinase conformational change
Supplementary Information Overlap between folding and functional energy landscapes for adenylate kinase conformational change by Ulrika Olsson & Magnus Wolf-Watz Contents: 1. Supplementary Note 2. Supplementary
More informationChirascan 6-Cell Peltier Cell Holder: Rapid Optimisation of Buffer Conditions for Stabilising Protein Therapeutics
CHIRASCAN SERIES APPLICATION NOTE Chirascan 6-Cell Peltier Cell Holder: Rapid Optimisation of Buffer Conditions for Stabilising Protein Therapeutics Abstract: The selection of buffer conditions that maximise
More informationPrinciples of Bioenergetics. Lehninger 3 rd ed. Chapter 14
1 Principles of Bioenergetics Lehninger 3 rd ed. Chapter 14 2 Metabolism A highly coordinated cellular activity aimed at achieving the following goals: Obtain chemical energy. Convert nutrient molecules
More informationShort Announcements. 1 st Quiz today: 15 minutes. Homework 3: Due next Wednesday.
Short Announcements 1 st Quiz today: 15 minutes Homework 3: Due next Wednesday. Next Lecture, on Visualizing Molecular Dynamics (VMD) by Klaus Schulten Today s Lecture: Protein Folding, Misfolding, Aggregation
More informationCD Basis Set of Spectra that is used is that derived from comparing the spectra of globular proteins whose secondary structures are known from X-ray
CD Basis Set of Spectra that is used is that derived from comparing the spectra of globular proteins whose secondary structures are known from X-ray crystallography An example of the use of CD Modeling
More informationSupplementary Information
Supplementary Information Adenosyltransferase Tailors and Delivers Coenzyme B 12 Dominique Padovani 1,2, Tetyana Labunska 2, Bruce A. Palfey 1, David P. Ballou 1 and Ruma Banerjee 1,2 * 1 Biological Chemistry
More informationSupporting Information
Supporting Information Symmetry of Charge Partitioning in Collisional and UV Photon-induced Dissociation of Protein Assemblies Sem Tamara,,$, Andrey Dyachenko,,$, Kyle L. Fort,,$ Alexander Makarov,,# Richard
More informationANSWER KEY. Chemistry 25 (Spring term 2015) Midterm Examination
Name ANSWER KEY Chemistry 25 (Spring term 2015) Midterm Examination 1 (15 pts) Short answers 1A (3 pts) Consider the following system at two time points A and B. The system is divided by a moveable partition.
More informationScience Science 249: Nature Struct. Biol. NSB l 3: NSB PNAS 96: NSB
Discussion Papers P16. Eriksson AE, Baase WA, Zhang X-J, Heinz DW, Blaber M, Baldwin EP, Matthews BW. (1992) Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic
More informationIV. SOLVATION - CLASSICAL THERMODYNAMICS - STABILITY
1 IV. SOLVATION - CLASSICAL THERMODYNAMICS - STABILITY 1. Driving forces in protein folding a. Hydrophobicity is the dominant force driving protein folding. Protein folding was initially thought to be
More informationschematic diagram; EGF binding, dimerization, phosphorylation, Grb2 binding, etc.
Lecture 1: Noncovalent Biomolecular Interactions Bioengineering and Modeling of biological processes -e.g. tissue engineering, cancer, autoimmune disease Example: RTK signaling, e.g. EGFR Growth responses
More informationCONFOCHECK. Innovation with Integrity. Infrared Protein Analysis FT-IR
CONFOCHECK Infrared Protein Analysis Innovation with Integrity FT-IR CONFOCHECK: FT-IR System for Protein Analytics FT-IR Protein Analysis Infrared spectroscopy measures molecular vibrations due to the
More informationa) Write the reaction that occurs (pay attention to and label ends correctly) 5 AGCTG CAGCT > 5 AGCTG 3 3 TCGAC 5
Chem 315 Applications Practice Problem Set 1.As you learned in Chem 315, DNA higher order structure formation is a two step process. The first step, nucleation, is entropically the least favorable. The
More informationC a h p a t p e t r e r 6 E z n y z m y e m s
Chapter 6 Enzymes 4. Examples of enzymatic reactions acid-base catalysis: give and take protons covalent catalysis: a transient covalent bond is formed between the enzyme and the substrate metal ion catalysis:
More informationGeneral Chemistry revisited
General Chemistry revisited A(g) + B(g) C(g) + D(g) We said that G = H TS where, eg, H = f H(C) + f H(D) - f H(A) - f H(B) G < 0 implied spontaneous to right G > 0 implied spontaneous to left In a very
More informationThermodynamics and Kinetics
Thermodynamics and Kinetics Lecture 12 Free Energy Applications NC State University Isolated system requires DS > 0 DS sys > 0 Isolated system: Entropy increases for any spontaneous process System and
More informationMembrane Proteins: 1. Integral proteins: 2. Peripheral proteins: 3. Amphitropic proteins:
Membrane Proteins: 1. Integral proteins: proteins that insert into/span the membrane bilayer; or covalently linked to membrane lipids. (Interact with the hydrophobic part of the membrane) 2. Peripheral
More informationChemistry and the material world Unit 4, Lecture 4 Matthias Lein
Chemistry and the material world 123.102 Unit 4, Lecture 4 Matthias Lein Gibbs ree energy Gibbs ree energy to predict the direction o a chemical process. Exergonic and endergonic reactions. Temperature
More informationSupporting Text Z = 2Γ 2+ + Γ + Γ [1]
Supporting Text RNA folding experiments are typically carried out in a solution containing a mixture of monovalent and divalent ions, usually MgCl 2 and NaCl or KCl. All three species of ions, Mg, M +
More informationEffect of Guanidine Hydrochloride on the Thermal Stability of Hen Egg White Lysozyme
Effect of Guanidine Hydrochloride on the Thermal Stability of Hen Egg White Lysozyme Thesis Submitted In partial fulfillment of the requirement for the degree of MASTER OF SCIENCE IN CHEMISTRY Submitted
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 informationDetermination of the thermodynamics of carbonic anhydrase acid-unfolding by titration calorimetry
Available online at www.sciencedirect.com J. Biochem. Biophys. Methods 70 (2008) 1043 1047 www.elsevier.com/locate/jbbm Determination of the thermodynamics of carbonic anhydrase acid-unfolding by titration
More informationChapter 19 Chemical Thermodynamics Entropy and free energy
Chapter 19 Chemical Thermodynamics Entropy and free energy Learning goals and key skills: Explain and apply the terms spontaneous process, reversible process, irreversible process, and isothermal process.
More informationExamples of Protein Modeling. Protein Modeling. Primary Structure. Protein Structure Description. Protein Sequence Sources. Importing Sequences to MOE
Examples of Protein Modeling Protein Modeling Visualization Examination of an experimental structure to gain insight about a research question Dynamics To examine the dynamics of protein structures To
More informationProtein-Ligand Interactions: hydrodynamics and calorimetry
Protein-Ligand Interactions: hydrodynamics and calorimetry Approach Stephen E. Harding Babur Z. Chowdhry OXFORD UNIVERSITY PRESS , New York Oxford University Press, 2001 978-0-19-963746-1 List of protocols
More informationEnergy, Enzymes, and Metabolism. Energy, Enzymes, and Metabolism. A. Energy and Energy Conversions. A. Energy and Energy Conversions
Energy, Enzymes, and Metabolism Lecture Series 6 Energy, Enzymes, and Metabolism B. ATP: Transferring Energy in Cells D. Molecular Structure Determines Enzyme Fxn Energy is the capacity to do work (cause
More information[Urea] (M) k (s -1 )
BMB178 Fall 2018 Problem Set 1 Due: 10/26/2018, noon Office hour: 10/25/2018, SFL GSR218 7 9 pm Problem 1. Transition state theory (20 points): Consider a unimolecular reaction where a substrate S is converted
More informationFLUORESCENCE STUDY ON TRYPTOPHAN POTASSIUM IODIDE INTERACTION
PROCEEDINGS OF THE YEREVAN STATE UNIVERSITY C h e m i s t r y a n d B i o l o g y 08, 5(), p. 75 79 FLUORESCENCE STUDY ON TRYPTOPHAN POTASSIUM IODIDE INTERACTION C h emistr y H. A. SHILAJYAN, K. R. GRIGORYAN
More informationPhotosynthetic autotrophs use the energy of sunlight to convert low-g CO 2 and H 2 O into energy-rich complex sugar molecules.
Chapters 7 & 10 Bioenergetics To live, organisms must obtain energy from their environment and use it to do the work of building and organizing cell components such as proteins, enzymes, nucleic acids,
More informationStructural effects of LacI variants
Structural effects of aci variants 1 of 6 10/9/2012 1:05 PM Structural effects of aci variants TMD Change[1] Y282D Reversion[2] Variant ssembly Y7 W/Wless[3] M42 I 62 W/Wless[3] I64 1 V66 1 71 2 73 3 H74
More informationProf. Jason Kahn Your Signature: Exams written in pencil or erasable ink will not be re-graded under any circumstances.
1 Biochemistry 461 February 16, 1995 Exam #1 Prof. Jason Kahn Your Printed Name: Your SS#: Your Signature: You have 75 minutes for this exam. Exams written in pencil or erasable ink will not be re-graded
More informationExam 3 Solutions. ClO g. At 200 K and a total pressure of 1.0 bar, the partial pressure ratio for the chlorine-containing compounds is p ClO2
Chemistry 360 Dr. Jean M. Standard Fall 2016 Name KEY Exam 3 Solutions 1.) (14 points) Consider the gas phase decomposition of chlorine dioxide, ClO 2, ClO 2 ( g) ClO ( g) + O ( g). At 200 K and a total
More informationDental Biochemistry EXAM I
Dental Biochemistry EXAM I August 29, 2005 In the reaction below: CH 3 -CH 2 OH -~ ethanol CH 3 -CHO acetaldehyde A. acetoacetate is being produced B. ethanol is being oxidized to acetaldehyde C. acetaldehyde
More informationEnergetics of chitooligosaccharide binding to pumpkin (Cucurbita maxima) phloem exudate Lectin
Chapter 3 Energetics of chitooligosaccharide binding to pumpkin (Cucurbita maxima) phloem exudate Lectin 50 Chapter 3 Energetics of 51 Summary Binding of chitooligosaccharides [(GlcNAc) 2-6 ] to pumpkin
More informationBen McFarland Department of Chemistry Seattle Pacific University. Designing Proteins. The Creative Potential of Enthalpy and Entropy
Ben McFarland Department of Chemistry Seattle Pacific University Designing Proteins The Creative Potential of Enthalpy and Entropy Proteins are chemical: they have defined atomic structures accessible
More information