Lecture 34 Protein Unfolding Thermodynamics
|
|
- Silvester Stokes
- 5 years ago
- Views:
Transcription
1 Physical Principles in Biology Biology 3550 Fall 2018 Lecture 34 Protein Unfolding Thermodynamics Wednesday, 21 November c David P. Goldenberg University of Utah goldenberg@biology.utah.edu
2 Clicker Question #1 What holiday falls on Thursday, 22 November 2018? A) Halloween B) Veterans Day C) Thanksgiving D) Christmas E) Kwanza F) Chanukah
3 Protein Unfolding: A Simplified Summary For small, single-domain proteins ( 100 amino acids), unfolding is well described as a two-state process: N U Partially folded molecules are rarely detected at equilibrium. Free energy profile for unfolding and refolding:
4 Entropy Change for Protein Unfolding For now, focus only on the polypeptide chain itself: The native protein is a (relatively) unique structure. The unfolded state is an ensemble of rapidly interconverting structures. From Boltzmann: S = k ln Ω (for a single molecule) For the native state, assume Ω N = 1, S N = 0. (A questionable assumption, but it turns out to not be so bad.) What about the unfolded state?
5 Rotatable Bonds in an Amino Acid Residue Amino acid residue Amino acid residue: Part of amino acid left in a polypeptide. Assume that each residue can take on 10 conformations in the unfolded state.
6 Why This isn t an Absurd Way to Estimate the Entropy Change Rotational isomers (rotamers) In both native and unfolded states, dihedral angles fluctuate around energy minima. In native state, most bonds are restricted to one minimum. In unfolded state, bonds can sample two or three minima. The rotational isomeric state approximation
7 Entropy Change for Protein Unfolding From Boltzmann: S = k ln Ω For the native state, assume Ω N = 1, S N = 0. For the unfolded state assume that each residue can take on 10 possible conformations. For two residues, Ω U = 10 2 For three residues, Ω U = 10 3 For n residues, Ω U = 10 n S for unfolding S = S U S N = k ln Ω U k ln Ω N = k ln Ω U Ω N = k ln 10 n
8 Clicker Question #2 Estimate S for a protein 100 amino-acid residues long. A) J/K B) J/K C) J/K D) J/K k = J/K
9 Entropy Change for Unfolding S = k ln 10 n = J/K ln ln = 100 ln 10 S = J/K 100 ln J/K
10 Entropy Change for Protein Unfolding From the previous slides: S = k ln 10 n n is the number of amino acid residues. Assumes 1 conformation for the native state and 10 conformations for each residue in the unfolded state. On a molar basis for n = 100 S = R ln = J/(mol K) ln = J/(mol K) Because it only considers polypeptide conformation, call this S conf. Corresponding free energy change at 298 K: T S conf = J/mol = 570 kj/mol Compare with the overall free energy change for unfolding, on the order of 30 kj/mol
11 Could We Measure the Conformational Entropy Change for Unfolding a Protein? Recall reversible isothermal compression of a gas: Weight Weight Weight Thermal Reservoir Thermal Reservoir Thermal Reservoir To measure entropy: Measure work required for reversible process, w rev. Since E = 0 and E = q + w, q rev = w rev S sys = q rev /T = w rev /T. For a protein, measure the work to go from the unfolded ensemble to a single conformation (at constant temperature).
12 Stretching an Unfolded Protein Entropically, the single stretched-out conformation is equivalent to the single folded conformation. Folded Unfolded ensemble Single conformation Stretched conformation is equivelent to unfolded ensemble, with respect to stabilizing interactions. Have to stretch very slowly, to ensure reversibility. Have to measure very small forces as a function of distance. w rev = Fdx
13 An Atomic Force Microscope (AFM) Usual purpose is to make images of surfaces. Very fine tip (a few nm in radius) held on flexible cantilever. Sample is scanned below probe. Movement of cantilever is monitored optically. Cantilever can be calibrated to measure force as a function of displacement. (spring constant)
14 Stretching an Unfolded Protein with AFM Stage is moved very slowly, as deflection of cantilever is monitored. Deflection represents force as a function of distance. Force integrated over distance gives w rev. S conf = w rev /T This experiment is anti-trivial! Results are consistent with calculation based on rotational isomers. Thompson, J. B., Hansma, H. G., Hansma, P. K. & Plaxco, K. W. (2002). J. Mol. Biol., 322,
15 Observed Thermodynamics for Protein Folding For a typical single-domain protein of 100 amino-acid residues at room temperature (300 K): G u : 5 kj/mol to 50 kj/mol H u : 0 kj/mol to 200 kj/mol S u : G u = H u T S u S u = H u G u T = 100 kj/mol 30 kj/mol 300 T S u = 230 J/(mol K)
16 Observed Thermodynamics for Protein Folding For our (hypothetical) example at room temperature (300 K): Measured experimentally for unfolding: G u = 30 kj/mol H u = 100 kj/mol S u = 230 J/(mol K) Estimated change in conformational entropy: S conf = J/(mol K) T S conf = 570 kj/mol What we need to explain: Why is S u S conf? Why is G u T S conf?
17 Thermodynamics of Transfer of a Non-polar Molecule to Water CH 4 CH 4 Methane in a non-polar solvent Methane in Water G tr = H tr T S tr G tr is positive because S tr is negative! (an entropically driven process). Water molecules become more ordered when a non-polar molecule is introduced. Non-polar groups buried in the interior of folded proteins become exposed to water on unfolding.
18 Transfer Free Energy versus Accessible Surface Area 10 8 Hydrocarbons Nonpolar amino-acid sidechains Polar amino-acid side chains Figure adapted from: F. M. Richards. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng., 6: ,
19 Thermodynamics of Non-polar Surface Transfer to Water At 300 K H tr = A np 7 J/mol S tr = A np 0.3 J/(mol K) T S tr = A np 90 J/mol G tr = A np 97 J/mol A np : Non-polar surface area (Å 2 ) transferred from non-polar environment to water. How does the surface area exposed to water change when a protein unfolds? Estimates are from transfer measurements summarized in: Baldwin, R. L. (1986). Proc. Natl. Acad. Sci., USA, 83, and Spolar, R. S., Livingstone, J. R. & Record, T. M. (1992). Biochemistry, 31,
20 Folded Structure of a Small Protein: Ribonuclease A
21 Solvent-accessible Surface of Folded Ribonuclease A
22 Solvent-accessible Surface of Unfolded Ribonuclease A (one representative conformation)
23 Change in Accessible Surface Area for Unfolding Folded (Å 2 ) Unfolded (Å 2 ) Difference (Å 2 ) Total 7,000 14,700 7,700 Non-polar 3,800 8,800 5,000 Polar 3,200 5,900 2,700
24 Thermodynamic Consequence of Non-polar Surface Area Exposed Upon Unfolding (Hydrophobic Effect) For 5, 000 Å 2 at 300 K H hyd = 35 kj/mol S hyd = 1, 500 J/(mol K) G hyd = 480 kj/mol
25 Contributions to Protein Unfolding Thermodynamics For protein of 100 amino-acid residues at 300 K: H kj/mol S J/(mol K) G kj/mol Conformational entropy 2, Hydrophobic effect 35-1, Other Overall Increase in conformational entropy is largely compensated for by decrease in water entropy associated with hydrophobic effect. What might other contributions to H be? Breaking protein hydrogen bonds. Exposure of polar surface area to water.
= (-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 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 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 informationLecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2-3: 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 informationFree energy, electrostatics, and the hydrophobic effect
Protein Physics 2016 Lecture 3, January 26 Free energy, electrostatics, and the hydrophobic effect Magnus Andersson magnus.andersson@scilifelab.se Theoretical & Computational Biophysics Recap Protein structure
More informationLecture 27 Thermodynamics: Enthalpy, Gibbs Free Energy and Equilibrium Constants
Physical Principles in Biology Biology 3550 Fall 2017 Lecture 27 Thermodynamics: Enthalpy, Gibbs Free Energy and Equilibrium Constants Wednesday, 1 November c David P. Goldenberg University of Utah goldenberg@biology.utah.edu
More informationThe protein folding problem consists of two parts:
Energetics and kinetics of protein folding The protein folding problem consists of two parts: 1)Creating a stable, well-defined structure that is significantly more stable than all other possible structures.
More informationProtein Folding & Stability. Lecture 11: Margaret A. Daugherty. Fall How do we go from an unfolded polypeptide chain to a
Lecture 11: Protein Folding & Stability Margaret A. Daugherty Fall 2004 How do we go from an unfolded polypeptide chain to a compact folded protein? (Folding of thioredoxin, F. Richards) Structure - Function
More informationMolecular dynamics simulations of anti-aggregation effect of ibuprofen. Wenling E. Chang, Takako Takeda, E. Prabhu Raman, and Dmitri Klimov
Biophysical Journal, Volume 98 Supporting Material Molecular dynamics simulations of anti-aggregation effect of ibuprofen Wenling E. Chang, Takako Takeda, E. Prabhu Raman, and Dmitri Klimov Supplemental
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 informationBiochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,
Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,
More informationProteins polymer molecules, folded in complex structures. Konstantin Popov Department of Biochemistry and Biophysics
Proteins polymer molecules, folded in complex structures Konstantin Popov Department of Biochemistry and Biophysics Outline General aspects of polymer theory Size and persistent length of ideal linear
More information= 16! = 16! W A = 3 = 3 N = = W B 3!3!10! = ΔS = nrln V. = ln ( 3 ) V 1 = 27.4 J.
Answer key: Q1A Both configurations are equally likely because the particles are non-interacting (i.e., the energy does not favor one configuration over another). For A M = 16 N = 6 W A = 16! 0.9 101 =
More informationBIOC : Homework 1 Due 10/10
Contact information: Name: Student # BIOC530 2012: Homework 1 Due 10/10 Department Email address The following problems are based on David Baker s lectures of forces and protein folding. When numerical
More informationLecture 11: Protein Folding & Stability
Structure - Function Protein Folding: What we know Lecture 11: Protein Folding & Stability 1). Amino acid sequence dictates structure. 2). The native structure represents the lowest energy state for a
More informationProtein Folding & Stability. Lecture 11: Margaret A. Daugherty. Fall Protein Folding: What we know. Protein Folding
Lecture 11: Protein Folding & Stability Margaret A. Daugherty Fall 2003 Structure - Function Protein Folding: What we know 1). Amino acid sequence dictates structure. 2). The native structure represents
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 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 informationSecond Law Applications. NC State University
Chemistry 433 Lecture 11 Second Law Applications NC State University Summary of entropy calculations In the last lecture we derived formula for the calculation of the entropy change as a function of temperature
More informationLecture 28 Thermodynamics: Gibbs Free Energy, Equilibrium Constants and the Entropy Change for a Bimolecular Reaction
Physical Principles in Biology Biology 3550 Fall 2017 Lecture 28 Thermodynamics: Gibbs Free Energy, Equilibrium Constants and the Entropy Change for a Bimolecular Reaction Monday, 6 November c David P.
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 informationProtein Folding In Vitro*
Protein Folding In Vitro* Biochemistry 412 February 29, 2008 [*Note: includes computational (in silico) studies] Fersht & Daggett (2002) Cell 108, 573. Some folding-related facts about proteins: Many small,
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 informationPhysical Principles in Biology Biology 3550/3551 Fall 2018
July 26, 2018 Draft Physical Principles in Biology Biology 3550/3551 Fall 2018 hapter 6: Formation of Biomolecular Structure David P. Goldenberg University of Utah goldenberg@biology.utah.edu c 2017 David
More informationMolecular Interactions F14NMI. Lecture 4: worked answers to practice questions
Molecular Interactions F14NMI Lecture 4: worked answers to practice questions http://comp.chem.nottingham.ac.uk/teaching/f14nmi jonathan.hirst@nottingham.ac.uk (1) (a) Describe the Monte Carlo algorithm
More informationMolecular Origin of Hydration Heat Capacity Changes of Hydrophobic Solutes: Perturbation of Water Structure around Alkanes
J. Phys. Chem. B 1997, 101, 11237-11242 11237 Molecular Origin of Hydration Heat Capacity Changes of Hydrophobic Solutes: Perturbation of Water Structure around Alkanes Bhupinder Madan and Kim Sharp* The
More informationSCORING. The exam consists of 5 questions totaling 100 points as broken down in this table:
UNIVERSITY OF CALIFORNIA, BERKELEY CHEM C130/MCB C100A MIDTERM EXAMINATION #2 OCTOBER 20, 2016 INSTRUCTORS: John Kuriyan and David Savage THE TIME LIMIT FOR THIS EXAMINATION: 1 HOUR 50 MINUTES SIGNATURE:
More informationQuiz 2 Morphology of Complex Materials
071003 Quiz 2 Morphology of Complex Materials 1) Explain the following terms: (for states comment on biological activity and relative size of the structure) a) Native State b) Unfolded State c) Denatured
More informationTHE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION
THE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION AND CALIBRATION Calculation of turn and beta intrinsic propensities. A statistical analysis of a protein structure
More informationMany proteins spontaneously refold into native form in vitro with high fidelity and high speed.
Macromolecular Processes 20. Protein Folding Composed of 50 500 amino acids linked in 1D sequence by the polypeptide backbone The amino acid physical and chemical properties of the 20 amino acids dictate
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 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 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 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 informationLecture 1. Conformational Analysis in Acyclic Systems
Lecture 1 Conformational Analysis in Acyclic Systems Learning Outcomes: by the end of this lecture and after answering the associated problems, you will be able to: 1. use Newman and saw-horse projections
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 informationBiochemistry Prof. S. DasGupta Department of Chemistry Indian Institute of Technology Kharagpur. Lecture - 06 Protein Structure IV
Biochemistry Prof. S. DasGupta Department of Chemistry Indian Institute of Technology Kharagpur Lecture - 06 Protein Structure IV We complete our discussion on Protein Structures today. And just to recap
More information6 Hydrophobic interactions
The Physics and Chemistry of Water 6 Hydrophobic interactions A non-polar molecule in water disrupts the H- bond structure by forcing some water molecules to give up their hydrogen bonds. As a result,
More informationSingle molecule force spectroscopy reveals a highly compliant helical
Supplementary Information Single molecule force spectroscopy reveals a highly compliant helical folding for the 30 nm chromatin fiber Maarten Kruithof, Fan-Tso Chien, Andrew Routh, Colin Logie, Daniela
More informationBiochemistry 530: Introduction to Structural Biology. Autumn Quarter 2014 BIOC 530
Biochemistry 530: Introduction to Structural Biology Autumn Quarter 2014 Course Information Course Description Graduate-level discussion of the structure, function, and chemistry of proteins and nucleic
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 informationAtomic and molecular interactions. Scanning probe microscopy.
Atomic and molecular interactions. Scanning probe microscopy. Balázs Kiss Nanobiotechnology and Single Molecule Research Group, Department of Biophysics and Radiation Biology 27. November 2013. 2 Atomic
More informationHomework #4 Physics 498Bio Spring 2012 Prof. Paul Selvin
Assigned Wednesday Feb. 22, 2012: Due Wednesday February 29, 10:30am. Hand in at start of class. Late homework is not accepted. (Solution sets will be posted shortly after deadline.) Note: Marco will give
More informationOther 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 informationJulian Hassinger Madeleine Jensen
UNIVERSITY OF CALIFORNIA, BERKELEY CHEM C130/MCB C100A MIDTERM EXAMINATION #2 October 22, 2014 INSTRUCTORS: John Kuriyan and David Savage THE TIME LIMIT FOR THIS EXAMINATION: 1 HOUR 50 MINUTES SIGNATURE:
More informationCHEM Exam 2 - March 3, 2017
CHEM 3530 - Exam 2 - March 3, 2017 Constants and Conversion Factors NA = 6.02x10 23 mol -1 R = 8.31 J/mol-K = 8.31 kpa-l/mol-k 1 bar = 100 kpa = 750 torr 1 kpa = 7.50 torr 1 J = 1 kpa-l 1 kcal = 4.18 kj
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 informationBiophysical Model Building
Biophysical Model Building Step 1: Come up with a hypothesis about how a system works How many binding sites? Is there cooperativity? Step 2: Translate the qualitative hypotheses into an observable mathematical
More informationBCMP 201 Protein biochemistry
BCMP 201 Protein biochemistry BCMP 201 Protein biochemistry with emphasis on the interrelated roles of protein structure, catalytic activity, and macromolecular interactions in biological processes. The
More information7.88J Protein Folding Problem Fall 2007
MIT OpenCourseWare http://ocw.mit.edu 7.88J Protein Folding Problem Fall 2007 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. Lecture Notes - 3 7.24/7.88J/5.48J
More informationNH 2. Biochemistry I, Fall Term Sept 9, Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter
Biochemistry I, Fall Term Sept 9, 2005 Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter 3.1-3.4. Key Terms: ptical Activity, Chirality Peptide bond Condensation reaction ydrolysis
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 informationMeasurements of interaction forces in (biological) model systems
Measurements of interaction forces in (biological) model systems Marina Ruths Department of Chemistry, UMass Lowell What can force measurements tell us about a system? Depending on the technique, we might
More informationChemistry 123: Physical and Organic Chemistry Topic 2: Thermochemistry
Recall the equation. w = -PΔV = -(1.20 atm)(1.02 L)( = -1.24 10 2 J -101 J 1 L atm Where did the conversion factor come from? Compare two versions of the gas constant and calculate. 8.3145 J/mol K 0.082057
More informationarxiv:cond-mat/ v1 [cond-mat.soft] 19 Mar 2001
Modeling two-state cooperativity in protein folding Ke Fan, Jun Wang, and Wei Wang arxiv:cond-mat/0103385v1 [cond-mat.soft] 19 Mar 2001 National Laboratory of Solid State Microstructure and Department
More informationChapter 19 Chemical Thermodynamics Entropy and free energy
Chapter 19 Chemical Thermodynamics Entropy and free energy Learning goals and key skills: Understand the meaning of spontaneous process, reversible process, irreversible process, and isothermal process.
More informationGuessing the upper bound free-energy difference between native-like structures. Jorge A. Vila
1 Guessing the upper bound free-energy difference between native-like structures Jorge A. Vila IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700- San Luis, Argentina Use
More informationProtein Folding. I. Characteristics of proteins. C α
I. Characteristics of proteins Protein Folding 1. Proteins are one of the most important molecules of life. They perform numerous functions, from storing oxygen in tissues or transporting it in a blood
More informationANSWER KEY. Chemistry 25 (Spring term 2017) Midterm Examination
Name ANSWER KEY Chemistry 25 (Spring term 2017) Midterm Examination Distributed Thursday, May 4, 2017 Due Thursday, May 11, 2017 by 1 pm in class or by 12:45 pm in 362 Broad a drop box will be left outside
More informationBIBC 100. Structural Biochemistry
BIBC 100 Structural Biochemistry http://classes.biology.ucsd.edu/bibc100.wi14 Papers- Dialogue with Scientists Questions: Why? How? What? So What? Dialogue Structure to explain function Knowledge Food
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 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 informationEntropy and Free Energy in Biology
Entropy and Free Energy in Biology Energy vs. length from Phillips, Quake. Physics Today. 59:38-43, 2006. kt = 0.6 kcal/mol = 2.5 kj/mol = 25 mev typical protein typical cell Thermal effects = deterministic
More informationEntropy online activity: accompanying handout I. Introduction
Entropy online activity: accompanying handout I. Introduction The goal of this activity is to provide insight into the ways modern science views the effects of temperature on chemical reactions, including
More informationBCH 4053 Spring 2003 Chapter 6 Lecture Notes
BCH 4053 Spring 2003 Chapter 6 Lecture Notes 1 CHAPTER 6 Proteins: Secondary, Tertiary, and Quaternary Structure 2 Levels of Protein Structure Primary (sequence) Secondary (ordered structure along peptide
More informationSecondary 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 informationIntroduction to Computational Structural Biology
Introduction to Computational Structural Biology Part I 1. Introduction The disciplinary character of Computational Structural Biology The mathematical background required and the topics covered Bibliography
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 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 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 informationModeling Biological Systems Opportunities for Computer Scientists
Modeling Biological Systems Opportunities for Computer Scientists Filip Jagodzinski RBO Tutorial Series 25 June 2007 Computer Science Robotics & Biology Laboratory Protein: πρώτα, "prota, of Primary Importance
More informationAN INVESTIGATION INTO THE DEPENDENCE OF EGG PROTEIN DENATURATION ON TEMPERATURE.
AN INVESTIGATION INTO THE DEPENDENCE OF EGG PROTEIN DENATURATION ON TEMPERATURE. Aim The aim of this investigation was to investigate how the rate of denaturation of egg white proteins is dependent on
More informationStructural investigation of single biomolecules
Structural investigation of single biomolecules NMR spectroscopy and X-ray crystallography are currently the most common techniques capable of determining the structures of biological macromolecules like
More informationSupporting Online Material for
www.sciencemag.org/cgi/content/full/309/5742/1868/dc1 Supporting Online Material for Toward High-Resolution de Novo Structure Prediction for Small Proteins Philip Bradley, Kira M. S. Misura, David Baker*
More informationMolecular Mechanics. I. Quantum mechanical treatment of molecular systems
Molecular Mechanics I. Quantum mechanical treatment of molecular systems The first principle approach for describing the properties of molecules, including proteins, involves quantum mechanics. For example,
More informationStructural energetics of serine protease inhibition*
Pure Appl. Chem., Vol. 71, No. 7, pp. 1207 1213, 1999. Printed in Great Britain. 1999 IUPAC Structural energetics of serine protease inhibition* Kenneth P. Murphy, Brian M. Baker, Stephen P. Edgcomb and
More informationBIOCHEMISTRY Unit 2 Part 4 ACTIVITY #6 (Chapter 5) PROTEINS
BIOLOGY BIOCHEMISTRY Unit 2 Part 4 ACTIVITY #6 (Chapter 5) NAME NAME PERIOD PROTEINS GENERAL CHARACTERISTICS AND IMPORTANCES: Polymers of amino acids Each has unique 3-D shape Vary in sequence of amino
More informationScaling Law for the Radius of Gyration of Proteins and Its Dependence on Hydrophobicity
Scaling Law for the Radius of Gyration of Proteins and Its Dependence on Hydrophobicity LIU HONG, JINZHI LEI Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, People s Republic
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 information1,2-Dienes: 1,2-Dienes have two double bonds both joined to a central carbon which is often represented by a dot: R 2 R 1 R 4
LETURE 2 Alkenes: In alkenes we make the σ-bonds between carbon atoms by overlapping sp 2 hybrid orbitals which have been produced by the hybridisation of one s and only two p orbitals. These sp 2 hybrids
More informationFolding of small proteins using a single continuous potential
JOURNAL OF CHEMICAL PHYSICS VOLUME 120, NUMBER 17 1 MAY 2004 Folding of small proteins using a single continuous potential Seung-Yeon Kim School of Computational Sciences, Korea Institute for Advanced
More informationAnnouncements & Lecture Points
Announcements & Lecture Points Homework 3 (Klaus Schulten s Lecture): Due Wednesday. Quiz returned, next homework on Wednesday. Today s Lecture: Protein Folding, Misfolding, Aggregation. Experimental Approach
More informationFoundations of Chemical Kinetics. Lecture 30: Transition-state theory in the solution phase
Foundations of Chemical Kinetics Lecture 30: Transition-state theory in the solution phase Marc R. Roussel Department of Chemistry and Biochemistry Transition-state theory in solution We revisit our original
More informationChpt 19: Chemical. Thermodynamics. Thermodynamics
CEM 152 1 Reaction Spontaneity Can we learn anything about the probability of a reaction occurring based on reaction enthaplies? in general, a large, negative reaction enthalpy is indicative of a spontaneous
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 informationLecture 14. Entropy relationship to heat
Lecture 14 Entropy relationship to heat Reading: Lecture 14, today: Chapter 7: 7.20 end Lecture 15, Wednesday: Ref. (2) 2/29/16 1 Hemoglobin and probability Oxygen binding molecule. Its quaternary structure
More informationCHAPTER 2. Structure and Reactivity: Acids and Bases, Polar and Nonpolar Molecules
CHAPTER 2 Structure and Reactivity: Acids and Bases, Polar and Nonpolar Molecules 2-1 Kinetics and Thermodynamics of Simple Chemical Processes Chemical thermodynamics: Is concerned with the extent that
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 informationChemistry 2000 Lecture 9: Entropy and the second law of thermodynamics
Chemistry 2000 Lecture 9: Entropy and the second law of thermodynamics Marc R. Roussel January 23, 2018 Marc R. Roussel Entropy and the second law January 23, 2018 1 / 29 States in thermodynamics The thermodynamic
More informationProtein structure forces, and folding
Harvard-MIT Division of Health Sciences and Technology HST.508: Quantitative Genomics, Fall 2005 Instructors: Leonid Mirny, Robert Berwick, Alvin Kho, Isaac Kohane Protein structure forces, and folding
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 informationIsothermal experiments characterize time-dependent aggregation and unfolding
1 Energy Isothermal experiments characterize time-dependent aggregation and unfolding Technical ote Introduction Kinetic measurements have, for decades, given protein scientists insight into the mechanisms
More informationAbstract. Introduction
In silico protein design: the implementation of Dead-End Elimination algorithm CS 273 Spring 2005: Project Report Tyrone Anderson 2, Yu Bai1 3, and Caroline E. Moore-Kochlacs 2 1 Biophysics program, 2
More informationMolecular Modelling. part of Bioinformatik von RNA- und Proteinstrukturen. Sonja Prohaska. Leipzig, SS Computational EvoDevo University Leipzig
part of Bioinformatik von RNA- und Proteinstrukturen Computational EvoDevo University Leipzig Leipzig, SS 2011 Protein Structure levels or organization Primary structure: sequence of amino acids (from
More informationOutline. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Unfolded Folded. What is protein folding?
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation By Jun Shimada and Eugine Shaknovich Bill Hawse Dr. Bahar Elisa Sandvik and Mehrdad Safavian Outline Background on protein
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 informationLecture 20. Chemical Potential
Lecture 20 Chemical Potential Reading: Lecture 20, today: Chapter 10, sections A and B Lecture 21, Wednesday: Chapter 10: 10 17 end 3/21/16 1 Pop Question 7 Boltzmann Distribution Two systems with lowest
More informationBIOC 530 Fall, 2011 BIOC 530
Fall, 2011 Course Information Course Description Graduate-level discussion of the structure, function, and chemistry of proteins and nucleic acids, control of enzymatic reactions. Please see the course
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 informationHelix Folding Simulations with Various Initial Conformations
1 796 Biophysical Journal Volume 66 June 1994 1796-1803 Helix Folding Simulations with Various Initial Conformations Shen-Shu Sung Research Institute, The Cleveland Clinic Foundation, Cleveland Ohio 44195
More information