Spring 2012 Lecture 10-12
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Heterogeneous Impacts of Protein-Stabilizing Osmolytes On
bioRxiv preprint doi: https://doi.org/10.1101/328922; this version posted May 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction Mrinmoy Mukherjee and Jagannath Mondal⇤ Tata Institute of Fundamental Research Hyderabad, 500107 India E-mail: [email protected],+914020203091 Abstract Osmolytes’ mechanism of protecting proteins against denaturation is a longstanding puzzle, further complicated by the complex diversities inherent in protein sequences. An emergent approach in understanding osmolytes’ mechanism of action towards biopoly- mer has been to investigate osmolytes’ interplay with hydrophobic interaction, the ma- jor driving force of protein folding. However, the crucial question is whether all these protein-stabilizing osmolytes display a single unified mechanism towards hydrophobic interactions. By simulating the hydrophobic collapse of a macromolecule in aqueous solutions of two such osmoprotectants, Glycine and Trimethyl N-oxide (TMAO), both of which are known to stabilize protein’s folded conformation, we here demonstrate that these two osmolytes can impart mutually contrasting effects towards hydropho- bic interaction. While TMAO preserves its protectant nature across diverse range of polymer-osmolyte interactions, glycine is found to display an interesting cross-over from being a protectant at weaker polymer-osmolyte interaction to a denaturant of hydrophobicity at stronger polymer-osmolyte interactions. A preferential-interaction analysis reveals that a subtle balance of conformation-dependent exclusion/binding of ⇤To whom correspondence should be addressed 1 bioRxiv preprint doi: https://doi.org/10.1101/328922; this version posted May 23, 2018. -
Protein Structure & Folding
6 Protein Structure & Folding To understand protein folding In the last chapter we learned that proteins are composed of amino acids Goal as a chemical equilibrium. linked together by peptide bonds. We also learned that the twenty amino acids display a wide range of chemical properties. In this chapter we will see Objectives that how a protein folds is determined by its amino acid sequence and that the three-dimensional shape of a folded protein determines its function by After this chapter, you should be able to: the way it positions these amino acids. Finally, we will see that proteins fold • describe the four levels of protein because doing so minimizes Gibbs free energy and that this minimization structure and the thermodynamic involves both making the most favorable bonds and maximizing disorder. forces that stabilize them. • explain how entropy (S) and enthalpy Proteins exhibit four levels of structure (H) contribute to Gibbs free energy. • use the equation ΔG = ΔH – TΔS The structure of proteins can be broken down into four levels of to determine the dependence of organization. The first is primary structure, the linear sequence of amino the favorability of a reaction on acids in the polypeptide chain. By convention, the primary sequence is temperature. written in order from the amino acid at the N-terminus (by convention • explain the hydrophobic effect and its usually on the left) to the amino acid at the C-terminus. The second level role in protein folding. of protein structure, secondary structure, is the local conformation adopted by stretches of contiguous amino acids. -
POLYMER STRUCTURE and CHARACTERIZATION Professor
POLYMER STRUCTURE AND CHARACTERIZATION Professor John A. Nairn Fall 2007 TABLE OF CONTENTS 1 INTRODUCTION 1 1.1 Definitions of Terms . 2 1.2 Course Goals . 5 2 POLYMER MOLECULAR WEIGHT 7 2.1 Introduction . 7 2.2 Number Average Molecular Weight . 9 2.3 Weight Average Molecular Weight . 10 2.4 Other Average Molecular Weights . 10 2.5 A Distribution of Molecular Weights . 11 2.6 Most Probable Molecular Weight Distribution . 12 3 MOLECULAR CONFORMATIONS 21 3.1 Introduction . 21 3.2 Nomenclature . 23 3.3 Property Calculation . 25 3.4 Freely-Jointed Chain . 27 3.4.1 Freely-Jointed Chain Analysis . 28 3.4.2 Comment on Freely-Jointed Chain . 34 3.5 Equivalent Freely Jointed Chain . 37 3.6 Vector Analysis of Polymer Conformations . 38 3.7 Freely-Rotating Chain . 41 3.8 Hindered Rotating Chain . 43 3.9 More Realistic Analysis . 45 3.10 Theta (Θ) Temperature . 47 3.11 Rotational Isomeric State Model . 48 4 RUBBER ELASTICITY 57 4.1 Introduction . 57 4.2 Historical Observations . 57 4.3 Thermodynamics . 60 4.4 Mechanical Properties . 62 4.5 Making Elastomers . 68 4.5.1 Diene Elastomers . 68 0 4.5.2 Nondiene Elastomers . 69 4.5.3 Thermoplastic Elastomers . 70 5 AMORPHOUS POLYMERS 73 5.1 Introduction . 73 5.2 The Glass Transition . 73 5.3 Free Volume Theory . 73 5.4 Physical Aging . 73 6 SEMICRYSTALLINE POLYMERS 75 6.1 Introduction . 75 6.2 Degree of Crystallization . 75 6.3 Structures . 75 Chapter 1 INTRODUCTION The topic of polymer structure and characterization covers molecular structure of polymer molecules, the arrangement of polymer molecules within a bulk polymer material, and techniques used to give information about structure or properties of polymers. -
Workshop 1 – Biochemistry (Chem 160)
Workshop 1 – Biochemistry (Chem 160) 1. Draw the following peptide at pH = 7 and make sure to include the overall charge, label the N- and C-terminus, the peptide bond and the -carbon. AVDKY Give the overall charge of the peptide at pH = 3 and 12. 2. Draw a titration curve for Arg, make sure to label the different points. Determine the pI for Arg. 3. Nonpolar solute + water = solution a. What is the S of the universe, system and surroundings? The S of the universe would decrease this is why it is not spontaneous, the S of the system would increase but to a lesser extent to which the S of the surrounding would decrease S universe = S system + S surroundings 4. What is the hydrophobic effect and explain why it is thermodynamically favorable. The hydrophobic effect is when hydrophobic molecules tend to clump together burying them and placing hydrophilic molecules on the outside. The reason this is thermodynamically favorable is because it frees caged water molecules when burying clumping the hydrophobic molecules together. 5. Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? Urea dissolves in water because when dissolving there is a net increase in entropy of the universe. The heat exchange, getting colder only reflects the enthalpy (H) component of the total energy change. The entropy change is high enough to offset the enthalpy component and to add up to an overall -G 6. A mutation that changes an alanine residue in the interior of a protein to valine is found to lead to a loss of activity. -
Ideal Chain Conformations and Statistics
ENAS 606 : Polymer Physics Chinedum Osuji 01.24.2013:HO2 Ideal Chain Conformations and Statistics 1 Overview Consideration of the structure of macromolecules starts with a look at the details of chain level chemical details which can impact the conformations adopted by the polymer. In the case of saturated carbon ◦ backbones, while maintaining the desired Ci−1 − Ci − Ci+1 bond angle of 112 , the placement of the final carbon in the triad above can occur at any point along the circumference of a circle, defining a torsion angle '. We can readily recognize the energetic differences as a function this angle, U(') such that there are 3 minima - a deep minimum corresponding the the trans state, for which ' = 0 and energetically equivalent gauche− and gauche+ states at ' = ±120 degrees, as shown in Fig 1. Figure 1: Trans, gauche- and gauche+ configurations, and their energetic sates 1.1 Static Flexibility The static flexibility of the chain in equilibrium is determined by the difference between the levels of the energy minima corresponding the gauche and trans states, ∆. If ∆ < kT , the g+, g− and t states occur with similar probability, and so the chain can change direction and appears as a random coil. If ∆ takes on a larger value, then the t conformations will be enriched, so the chain will be rigid locally, but on larger length scales, the eventual occurrence of g+ and g− conformations imparts a random conformation. Overall, if we ignore details on some length scale smaller than lp, the persistence length, the polymer appears as a continuous flexible chain where 1 lp = l0 exp(∆/kT ) (1) where l0 is something like a monomer length. -
Native-Like Mean Structure in the Unfolded Ensemble of Small Proteins
B doi:10.1016/S0022-2836(02)00888-4 available online at http://www.idealibrary.com on w J. Mol. Biol. (2002) 323, 153–164 Native-like Mean Structure in the Unfolded Ensemble of Small Proteins Bojan Zagrovic1, Christopher D. Snow1, Siraj Khaliq2 Michael R. Shirts2 and Vijay S. Pande1,2* 1Biophysics Program The nature of the unfolded state plays a great role in our understanding of Stanford University, Stanford proteins. However, accurately studying the unfolded state with computer CA 94305-5080, USA simulation is difficult, due to its complexity and the great deal of sampling required. Using a supercluster of over 10,000 processors we 2Department of Chemistry have performed close to 800 ms of molecular dynamics simulation in Stanford University, Stanford atomistic detail of the folded and unfolded states of three polypeptides CA 94305-5080, USA from a range of structural classes: the all-alpha villin headpiece molecule, the beta hairpin tryptophan zipper, and a designed alpha-beta zinc finger mimic. A comparison between the folded and the unfolded ensembles reveals that, even though virtually none of the individual members of the unfolded ensemble exhibits native-like features, the mean unfolded structure (averaged over the entire unfolded ensemble) has a native-like geometry. This suggests several novel implications for protein folding and structure prediction as well as new interpretations for experiments which find structure in ensemble-averaged measurements. q 2002 Elsevier Science Ltd. All rights reserved Keywords: mean-structure hypothesis; unfolded state of proteins; *Corresponding author distributed computing; conformational averaging Introduction under folding conditions, with some notable exceptions.14 – 16 This is understandable since under Historically, the unfolded state of proteins has such conditions the unfolded state is an unstable, received significantly less attention than the folded fleeting species making any kind of quantitative state.1 The reasons for this are primarily its struc- experimental measurement very difficult. -
2. Proteins Have Hierarchies of Structure
27 2. Proteins have Hierarchies of Structure Protein structure is usually described at four different levels (Fig. II.2.1). The first level, called the primary structure, describes the linear sequence of the amino acids in the chain. The different primary structures correspond to the different sequences in which the amino acids are covalently linked together. The secondary structure describes two common patterns of structural repetition in proteins: the coiling up into helices of segments of the chain, and the pairing together of strands of the chain into β-sheets. The tertiary structure is the next higher level of organization, the overall arrangement of secondary structural elements. The quaternary structure describes how different polypeptide chains are assembled into complexes. Figure II.2.1. Different levels of protein structure. A protein chain’s primary structure is its amino acid sequence. Secondary structure consists of the regular organization of helices and sheets. The example shown is a schematic representation of an α helix. Tertiary structure is a polypeptide chain’s three- dimensional native conformation, which often involves compact packing of secondary structure elements. The example given in the figure is a schematic drawing of one of the four polypeptide chains (subunits) of hemoglobin, the protein that transports oxygen in the blood. α-helices along the chain are represented as cylinders. N is the amino terminus and C is the carboxyl terminus of the polypeptide chain. Quaternary structure is the arrangement of multiple polypeptide chains (subunits) to form a functional biomolecular structure. The figure shows the quaternary arrangement of four subunits to form the functional hemoglobin molecule. -
Hydrophobic Effect, Water Structure, and Heat Capacity Changes
J. Phys. Chem. B 1997, 101, 4343-4348 4343 Hydrophobic Effect, Water Structure, and Heat Capacity Changes Kim A. Sharp* and Bhupinder Madan Department of Biochemistry & Biophysics, UniVersity of PennsylVania, 3700 Hamilton Walk, Philadelphia, PennsylVania 19104-6059 ReceiVed: January 16, 1997; In Final Form: April 1, 1997X hyd The hydration heat capacity (∆Cp ) of nine solutes of varying hydrophobicity was studied using a combination of a random network model equation of water and Monte Carlo simulations. Nonpolar solutes cause a concerted decrease in the average length and angle of the water-water hydrogen bonds in the first hydration shell, while polar and ionic solutes have the opposite effect. This is due to changes in the amounts, relative to bulk water, of two populations of hydrogen bonds: one with shorter and more linear bonds and the other with longer and more bent bonds. Heat capacity changes were calculated from these changes in water structure using a random network model equation of state. The calculated changes account for observed hyd differences in ∆Cp for the various solutes. The simulations provide a unified picture of hydrophobic and hyd polar hydration, and both a structural and thermodynamic explanation of the opposite signs of ∆Cp observed for polar and nonpolar solutes. Introduction nonpolar groups means that at higher temperatures (T > 80 °C) their insolubility results from unfavorable changes in enthalpy, In recent years analysis of heat capacity changes has become not entropy. Second, the hydration of a majority of polar and of central importance in understanding the thermodynamics of ionic solutes is also accompanied by a decrease in entropy, and protein folding, protein-protein binding, protein-nucleic acid thus by some kind of structuring of water, but in this case binding, and the hydrophobic effect.1-7 There are several hyd 7,16-20 reasons for this. -
Packing of Secondary Structures II
7.88 Lecture Notes - 5 7.24/7.88J/5.48J The Protein Folding and Human Disease Packing of Secondary Structures • Packing of Helices against sheets • Packing of sheets against sheets • Parallel • Orthogonal Table: “Amino Acid Composition of the Ten Proteins and of the Residues at the Helix to Helix Interfaces” Name Total % Total At contacts % at contacts Gly 182 9 15 4 Ala 191 9 49 12 Val 151 7 46 12 Leu 148 7 48 12 Ile 114 6 36 9 Pro 67 3 41 1 Phe 68 3 25 6 Tyr 87 6 14 4 Trp 35 2 7 2 His 45 2 18 5 ½Cys 21 1 3 1 Met 29 1 10 3 Ser 165 8 19 5 Thr 132 7 21 5 Asp 112 6 14 4 Asn 113 6 13 3 Glu 94 5 13 3 Gln 70 3 12 3 Lys 125 6 19 5 Arg 76 4 13 3 A. Factors Contributing to Stability of Correctly Folded Native State 1. Major source of stability = removal of hydrophobic side chains atoms from the solvent and burying in environment which excludes the solvent (Entropic contribution from water structure). 1 2. Formation of hydrogen bonds between buried amide and carbonyl groups is maximized 3. Retention of backbone conformations close to the minimal energies. 4. Close packing means optimal Van der Waals interactions. You have read about alpha/beta proteins in Brandon and Tooze. B. Helix to Sheet Packing Lets examine buried contacts between the helices and the sheets. First a quick review of beta sheet structure: Colored transparency: Theoretical model, not actual sheet. -
Amino Acid Preference Against Beta Sheet Through Allowing Backbone Hydration Enabled by the Presence of Cation
Amino acid preference against beta sheet through allowing backbone hydration enabled by the presence of cation John N. Sharley, University of Adelaide. arXiv 2016-10-03 [email protected] Table of Contents 1 Abstract 1 2 Introduction 2 2.1 Alpha helix preferring amino acid residues in a beta sheet 2 2.2 Cation interactions with protein backbone oxygen 3 2.3 Quantum molecular dynamics with quantum mechanical treatment of every water molecule 3 3 Methods 4 4 Results 5 4.1 Preparation 5 4.2 Experiment 1302 5 4.3 Experiment 1303 7 5 Discussion 9 5.1 HB networks of water 9 5.2 Subsequent to rupture of a transient beta sheet 9 5.3 Hofmeister effects 10 6 Conclusion 11 7 Future work 12 8 Acknowledgements 13 9 References 14 10 Appendix 1. Backbone hydration in experiment 1302 16 11 Appendix 2. Backbone hydration in experiment 1303 17 1 Abstract It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference [1]. The present observations with Quantum Molecular Dynamics, QMD, simulation with Quantum Mechanical, QM, treatment of every water molecule solvating a beta sheet that would be transient in nature suggest that this steric blocking is not applicable in a hydrophobic region unless a cation is present, so that the amino acid beta sheet preference due to this steric blocking is only effective in the presence of a cation. We observed backbone hydration in a polyalanine and to a lesser extent polyvaline alpha helix without a cation being present, but a cation could increase the strength of these HBs. -
CD of Proteins Sources Include
LSM, updated 3/26/12 Some General Information on CD of Proteins Sources include: http://www.ap-lab.com/circular_dichroism.htm Far-UV range (190-250nm) Secondary structure can be determined by CD spectroscopy in the far-UV region. At these wavelengths the chromophore is the peptide bond, and the signal arises when it is located in a regular, folded environment. Alpha-helix, beta-sheet, and random coil structures each give rise to a characteristic shape and magnitude of CD spectrum. This is illustrated by the graph below, which shows spectra for poly-lysine in these three different conformations. • Alpha helix has negative bands at 222nm and 208nm and a positive one at 190nm. • Beta sheet shows a negative band at 218 nm and a positive one at 196 nm. • Random coil has a positive band at 212 nm and a negative one around 195 nm. The approximate fraction of each secondary structure type that is present in any protein can thus be determined by analyzing its far-UV CD spectrum as a sum of fractional multiples of such reference spectra for each structural type. (e.g. For an alpha helical protein with increasing amounts of random coil present, the 222 nm minimum becomes shallower and the 208 nm minimum moves to lower wavelengths ⇒ black spectrum + increasing contributions from green spectrum.) Like all spectroscopic techniques, the CD signal reflects an average of the entire molecular population. Thus, while CD can determine that a protein contains about 50% alpha-helix, it cannot determine which specific residues are involved in the helical portion. -
A Switch Between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants
A Switch Between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants Pehr B. Harbury; Tao Zhang; Peter S. Kim; Tom Alber Science, New Series, Vol. 262, No. 5138. (Nov. 26, 1993), pp. 1401-1407. Stable URL: http://links.jstor.org/sici?sici=0036-8075%2819931126%293%3A262%3A5138%3C1401%3AASBTTA%3E2.0.CO%3B2-H Science is currently published by American Association for the Advancement of Science. Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available at http://www.jstor.org/about/terms.html. JSTOR's Terms and Conditions of Use provides, in part, that unless you have obtained prior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content in the JSTOR archive only for your personal, non-commercial use. Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained at http://www.jstor.org/journals/aaas.html. Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printed page of such transmission. The JSTOR Archive is a trusted digital repository providing for long-term preservation and access to leading academic journals and scholarly literature from around the world. The Archive is supported by libraries, scholarly societies, publishers, and foundations. It is an initiative of JSTOR, a not-for-profit organization with a mission to help the scholarly community take advantage of advances in technology. For more information regarding JSTOR, please contact [email protected].