Thermodynamic and Extrathermodynamic Requirements of Enzyme Catalysis
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Arginine Kinase: a Crystallographic Investigation of Essential Substrate Structure Shawn A
Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2006 Arginine Kinase: A Crystallographic Investigation of Essential Substrate Structure Shawn A. (Shawn Adam) Clark Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES ARGININE KINASE; A CRYSTALLOGRAPHIC INVESTIGATION OF ESSENTIAL SUBSTRATE STRUCTURE BY SHAWN A. CLARK A Dissertation submitted to the Department of Chemistry and Biochemistry In partial fulfillment of the requirements for the Degree of Doctor of Philosophy Degree Awarded: Fall Semester, 2006 The members of committee approve the dissertation of Shawn A. Clark defended on 11/2/2006 __________________ Michael Chapman Professor Co-Directing Dissertation __________________ Tim Logan Professor Co-Directing Dissertation __________________ Ross Ellington Outside Committee Member __________________ Al Stiegman Committee Member _________________ Tim Cross Committee Member Approved: ________________________________________ Naresh Dalal, Department Chair, Department of Chemistry & Biochemistry The Office of Graduate Studies has verified and approved the above named committee members. ii ACKNOWLEDGEMENTS The voyage through academic maturity is full of numerous challenges that present themselves at many levels: physically, mentally, and emotionally. These hurdles can only be overcome with dedication, guidance, patience and above all support. It is for these reasons that I would like to express my sincerest and deepest admiration and love for my family; my wife Bobbi, and my two children Allexis and Brytney. Their encouragement, sacrifice, patience, loving support, and inquisitive nature have been the pillar of my strength, the beacon of my determination, and the spark of my intuition. -
Biochemistry and the Genomic Revolution 1.1
Dedication About the authors Preface Tools and Techniques Clinical Applications Molecular Evolution Supplements Supporting Biochemistry, Fifth Edition Acknowledgments I. The Molecular Design of Life 1. Prelude: Biochemistry and the Genomic Revolution 1.1. DNA Illustrates the Relation between Form and Function 1.2. Biochemical Unity Underlies Biological Diversity 1.3. Chemical Bonds in Biochemistry 1.4. Biochemistry and Human Biology Appendix: Depicting Molecular Structures 2. Biochemical Evolution 2.1. Key Organic Molecules Are Used by Living Systems 2.2. Evolution Requires Reproduction, Variation, and Selective Pressure 2.3. Energy Transformations Are Necessary to Sustain Living Systems 2.4. Cells Can Respond to Changes in Their Environments Summary Problems Selected Readings 3. Protein Structure and Function 3.1. Proteins Are Built from a Repertoire of 20 Amino Acids 3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops 3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores 3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures 3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure Summary Appendix: Acid-Base Concepts Problems Selected Readings 4. Exploring Proteins 4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation 4.3. Immunology Provides Important Techniques with Which to Investigate Proteins 4.4. Peptides Can Be Synthesized by Automated Solid-Phase Methods 4.5. -
Chapter 9. Atomic Transport Properties
NEA/NSC/R(2015)5 Chapter 9. Atomic transport properties M. Freyss CEA, DEN, DEC, Centre de Cadarache, France Abstract As presented in the first chapter of this book, atomic transport properties govern a large panel of nuclear fuel properties, from its microstructure after fabrication to its behaviour under irradiation: grain growth, oxidation, fission product release, gas bubble nucleation. The modelling of the atomic transport properties is therefore the key to understanding and predicting the material behaviour under irradiation or in storage conditions. In particular, it is noteworthy that many modelling techniques within the so-called multi-scale modelling scheme of materials make use of atomic transport data as input parameters: activation energies of diffusion, diffusion coefficients, diffusion mechanisms, all of which are then required to be known accurately. Modelling approaches that are readily used or which could be used to determine atomic transport properties of nuclear materials are reviewed here. They comprise, on the one hand, static atomistic calculations, in which the migration mechanism is fixed and the corresponding migration energy barrier is calculated, and, on the other hand, molecular dynamics calculations and kinetic Monte-Carlo simulations, for which the time evolution of the system is explicitly calculated. Introduction In nuclear materials, atomic transport properties can be a combination of radiation effects (atom collisions) and thermal effects (lattice vibrations), this latter being possibly enhanced by vacancies created by radiation damage in the crystal lattice (radiation enhanced-diffusion). Thermal diffusion usually occurs at high temperature (typically above 1 000 K in nuclear ceramics), which makes the transport processes difficult to model at lower temperatures because of the low probability to see the diffusion event occur in a reasonable simulation time. -
Transition State Theory. I
MIT OpenCourseWare http://ocw.mit.edu 5.62 Physical Chemistry II Spring 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. 5.62 Spring 2007 Lecture #33 Page 1 Transition State Theory. I. Transition State Theory = Activated Complex Theory = Absolute Rate Theory ‡ k H2 + F "! [H2F] !!" HF + H Assume equilibrium between reactants H2 + F and the transition state. [H F]‡ K‡ = 2 [H2 ][F] Treat the transition state as a molecule with structure that decays unimolecularly with rate constant k. d[HF] ‡ ‡ = k[H2F] = kK [H2 ][F] dt k has units of sec–1 (unimolecular decay). The motion along the reaction coordinate looks ‡ like an antisymmetric vibration of H2F , one-half cycle of this vibration. Therefore k can be approximated by the frequency of the antisymmetric vibration ν[sec–1] k ≈ ν ≡ frequency of antisymmetric vibration (bond formation and cleavage looks like antisymmetric vibration) d[HF] = νK‡ [H2] [F] dt ! ‡* $ d[HF] (q / N) 'E‡ /kT [ ] = ν # *H F &e [H2 ] F dt "#(q 2 N)(q / N)%& ! ‡ $ ‡ ‡* ‡ (q / N) ' q *' q *' g * ‡ K‡ = # trans &) rot ,) vib ,) 0 ,e-E kT H2 qH2 ) q*H2 , gH2 gF "# (qtrans N) %&( rot +( vib +( 0 0 + ‡ Reaction coordinate is antisymmetric vibrational mode of H2F . This vibration is fully excited (high T limit) because it leads to the cleavage of the H–H bond and the formation of the H–F bond. For a fully excited vibration hν kT The vibrational partition function for the antisymmetric mode is revised 4/24/08 3:50 PM 5.62 Spring 2007 Lecture #33 Page 2 1 kT q*asym = ' since e–hν/kT ≈ 1 – hν/kT vib 1! e!h" kT h! Note that this is an incredibly important simplification. -
Eyring Equation
Search Buy/Sell Used Reactors Glass microreactors Hydrogenation Reactor Buy Or Sell Used Reactors Here. Save Time Microreactors made of glass and lab High performance reactor technology Safe And Money Through IPPE! systems for chemical synthesis scale-up. Worldwide supply www.IPPE.com www.mikroglas.com www.biazzi.com Reactors & Calorimeters Induction Heating Reacting Flow Simulation Steam Calculator For Process R&D Laboratories Check Out Induction Heating Software & Mechanisms for Excel steam table add-in for water Automated & Manual Solutions From A Trusted Source. Chemical, Combustion & Materials and steam properties www.helgroup.com myewoss.biz Processes www.chemgoodies.com www.reactiondesign.com Eyring Equation Peter Keusch, University of Regensburg German version "If the Lord Almighty had consulted me before embarking upon the Creation, I should have recommended something simpler." Alphonso X, the Wise of Spain (1223-1284) "Everything should be made as simple as possible, but not simpler." Albert Einstein Both the Arrhenius and the Eyring equation describe the temperature dependence of reaction rate. Strictly speaking, the Arrhenius equation can be applied only to the kinetics of gas reactions. The Eyring equation is also used in the study of solution reactions and mixed phase reactions - all places where the simple collision model is not very helpful. The Arrhenius equation is founded on the empirical observation that rates of reactions increase with temperature. The Eyring equation is a theoretical construct, based on transition state model. The bimolecular reaction is considered by 'transition state theory'. According to the transition state model, the reactants are getting over into an unsteady intermediate state on the reaction pathway. -
Biographical References for Nobel Laureates
Dr. John Andraos, http://www.careerchem.com/NAMED/Nobel-Biographies.pdf 1 BIOGRAPHICAL AND OBITUARY REFERENCES FOR NOBEL LAUREATES IN SCIENCE © Dr. John Andraos, 2004 - 2021 Department of Chemistry, York University 4700 Keele Street, Toronto, ONTARIO M3J 1P3, CANADA For suggestions, corrections, additional information, and comments please send e-mails to [email protected] http://www.chem.yorku.ca/NAMED/ CHEMISTRY NOBEL CHEMISTS Agre, Peter C. Alder, Kurt Günzl, M.; Günzl, W. Angew. Chem. 1960, 72, 219 Ihde, A.J. in Gillispie, Charles Coulston (ed.) Dictionary of Scientific Biography, Charles Scribner & Sons: New York 1981, Vol. 1, p. 105 Walters, L.R. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 328 Sauer, J. Chem. Ber. 1970, 103, XI Altman, Sidney Lerman, L.S. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 737 Anfinsen, Christian B. Husic, H.D. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 532 Anfinsen, C.B. The Molecular Basis of Evolution, Wiley: New York, 1959 Arrhenius, Svante J.W. Proc. Roy. Soc. London 1928, 119A, ix-xix Farber, Eduard (ed.), Great Chemists, Interscience Publishers: New York, 1961 Riesenfeld, E.H., Chem. Ber. 1930, 63A, 1 Daintith, J.; Mitchell, S.; Tootill, E.; Gjersten, D., Biographical Encyclopedia of Scientists, Institute of Physics Publishing: Bristol, UK, 1994 Fleck, G. in James, Laylin K. (ed.), Nobel Laureates in Chemistry 1901 - 1992, American Chemical Society: Washington, DC, 1993, p. 15 Lorenz, R., Angew. -
Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium Sp
Article Cite This: Biochemistry 2019, 58, 1246−1259 pubs.acs.org/biochemistry Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium sp. TCM1 † † † ‡ ‡ Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge,*, † and Frank M. Raushel*, † Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States ‡ Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States *S Supporting Information ABSTRACT: Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phospho- triesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organo- phosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and ff ff secondary 18-oxygen isotope e ects on substrate hydrolysis and a determination of the e ects of changing the pKa of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. -
Effect of Enzyme/Substrate Ratio on the Antioxidant Properties of Hydrolysed African Yam Bean
African Journal of Biotechnology Vol. 11(50), pp. 11086-11091, 21 June, 2012 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB11.2271 ISSN 1684–5315 ©2012 Academic Journals Full Length Research Paper Effect of enzyme/substrate ratio on the antioxidant properties of hydrolysed African yam bean Fasasi Olufunmilayo*, Oyebode Esther and Fagbamila Oluwatoyin Department of Food Science and Technology, P. M. B. 704, Federal University of Technology, Akure, Nigeria. Accepted 8 June, 2012 The use of natural antioxidant as compared with synthetic antioxidant in food processing is a growing trend as consumers prefer natural to synthetic antioxidant mainly on emotional ground. This study investigates the antioxidant activity of hydrolysed African yam bean (Sphenostylis sternocarpa) which is regarded as one of the neglected underutilized species (NUS) of crop in Africa and Nigeria especially to improve food security and boost the economic importance of the crop. The antioxidant properties of African yam bean hydrolysates (AYH) produced at different enzyme to substrate (E/S) ratios of 1: 100 and 3: 100 (W/V) using pepsin (pH 2.0, 37°C) were studied. 2, 2-Diphenyl-1-picryl-hydrazyl (DPPH) radical scavenging activity of the hydrolysates was significantly influenced by the E\S ratio as DPPH radical scavenging activity ranged from 56.1 to 75.8% in AYH (1: 100) and 33.3 to 58.8% in AYH (3:100) with 1000 µg/ml having the highest DPPH radical scavenging activity. AYH (1:100) and AYH (3:100) had higher reducing activities of 0.42 and 0.23, respectively at a concentration of 1000 µg/ml. -
Regulation of Energy Substrate Metabolism in Endurance Exercise
International Journal of Environmental Research and Public Health Review Regulation of Energy Substrate Metabolism in Endurance Exercise Abdullah F. Alghannam 1,* , Mazen M. Ghaith 2 and Maha H. Alhussain 3 1 Lifestyle and Health Research Center, Health Sciences Research Center, Princess Nourah bInt. Abdulrahman University, Riyadh 84428, Saudi Arabia 2 Faculty of Applied Medical Sciences, Laboratory Medicine Department, Umm Al-Qura University, Al Abdeyah, Makkah 7607, Saudi Arabia; [email protected] 3 Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; [email protected] * Correspondence: [email protected] Abstract: The human body requires energy to function. Adenosine triphosphate (ATP) is the cellular currency for energy-requiring processes including mechanical work (i.e., exercise). ATP used by the cells is ultimately derived from the catabolism of energy substrate molecules—carbohydrates, fat, and protein. In prolonged moderate to high-intensity exercise, there is a delicate interplay between carbohydrate and fat metabolism, and this bioenergetic process is tightly regulated by numerous physiological, nutritional, and environmental factors such as exercise intensity and du- ration, body mass and feeding state. Carbohydrate metabolism is of critical importance during prolonged endurance-type exercise, reflecting the physiological need to regulate glucose homeostasis, assuring optimal glycogen storage, proper muscle fuelling, and delaying the onset of fatigue. Fat metabolism represents a sustainable source of energy to meet energy demands and preserve the ‘limited’ carbohydrate stores. Coordinated neural, hormonal and circulatory events occur during prolonged endurance-type exercise, facilitating the delivery of fatty acids from adipose tissue to the Citation: Alghannam, A.F.; Ghaith, working muscle for oxidation. -
Lecture Outline a Closer Look at Carbocation Stabilities and SN1/E1 Reaction Rates We Learned That an Important Factor in the SN
Lecture outline A closer look at carbocation stabilities and SN1/E1 reaction rates We learned that an important factor in the SN1/E1 reaction pathway is the stability of the carbocation intermediate. The more stable the carbocation, the faster the reaction. But how do we know anything about the stabilities of carbocations? After all, they are very unstable, high-energy species that can't be observed directly under ordinary reaction conditions. In protic solvents, carbocations typically survive only for picoseconds (1 ps - 10–12s). Much of what we know (or assume we know) about carbocation stabilities comes from measurements of the rates of reactions that form them, like the ionization of an alkyl halide in a polar solvent. The key to connecting reaction rates (kinetics) with the stability of high-energy intermediates (thermodynamics) is the Hammond postulate. The Hammond postulate says that if two consecutive structures on a reaction coordinate are similar in energy, they are also similar in structure. For example, in the SN1/E1 reactions, we know that the carbocation intermediate is much higher in energy than the alkyl halide reactant, so the transition state for the ionization step must lie closer in energy to the carbocation than the alkyl halide. The Hammond postulate says that the transition state should therefore resemble the carbocation in structure. So factors that stabilize the carbocation also stabilize the transition state leading to it. Here are two examples of rxn coordinate diagrams for the ionization step that are reasonable and unreasonable according to the Hammond postulate. We use the Hammond postulate frequently in making assumptions about the nature of transition states and how reaction rates should be influenced by structural features in the reactants or products. -
Antibodies with Some Bite Antibodies Have Yet to Be Determined, It Is Reasonable to Suppose That the Ester Or David E
-~-------------------------------------N8NSANDVIEWS----------------_N_A_TU_R_E_V-O_L_._32_5_22_J_A_N_U_A_RY__ 19~87 Enzyme catalysis kinetics and is subject to competitive inhibition. Although the detailed chemical mechanisms of these catalytic Antibodies with some bite antibodies have yet to be determined, it is reasonable to suppose that the ester or David E. Hansen carbamate is strained towards a tetra hedral geometry on binding, thus facilitat THE spectacular specificities and rate William Jencks', more directly, stated in ing the attack of the hydroxide ion. Fur enhancements of enzymes are without 1969 thermore, the Scripps group has already equal among all known catalysts. It is no If complementarity between active site and found that their antibody can act via both wonder then that the design of new en transition state contributes significantly to nucleophilic and general base catalysis, zymes has long been a goal of biochemists. enzyme catalysis, it should be possible to syn depending on the substrate used. Now two independent groups, one led by thesize an enzyme by constructing a binding The fact that this approach succeeded at Alfonso Tramontano and Richard Lerner site. One way to do this is to prepare an anti all gives great hope to those attempting to of the Scripps Clinic and Research Foun body to a haptenic group which resembles the isolate even more efficient antibody cat dation', and the other by Peter Schultz of transition state of a given reaction. The com alysts by this and by other strategies. In the University of California at Berkeley\ bining sites of such antibodies should be com addition, it may be possible to modify have taken steps towards this goal by plementary to the transition state and should cause an acceleration by forcing bound sub existing catalytic antibodies. -
Glossary of Terms Used in Photochemistry, 3Rd Edition (IUPAC
Pure Appl. Chem., Vol. 79, No. 3, pp. 293–465, 2007. doi:10.1351/pac200779030293 © 2007 IUPAC INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY ORGANIC AND BIOMOLECULAR CHEMISTRY DIVISION* SUBCOMMITTEE ON PHOTOCHEMISTRY GLOSSARY OF TERMS USED IN PHOTOCHEMISTRY 3rd EDITION (IUPAC Recommendations 2006) Prepared for publication by S. E. BRASLAVSKY‡ Max-Planck-Institut für Bioanorganische Chemie, Postfach 10 13 65, 45413 Mülheim an der Ruhr, Germany *Membership of the Organic and Biomolecular Chemistry Division Committee during the preparation of this re- port (2003–2006) was as follows: President: T. T. Tidwell (1998–2003), M. Isobe (2002–2005); Vice President: D. StC. Black (1996–2003), V. T. Ivanov (1996–2005); Secretary: G. M. Blackburn (2002–2005); Past President: T. Norin (1996–2003), T. T. Tidwell (1998–2005) (initial date indicates first time elected as Division member). The list of the other Division members can be found in <http://www.iupac.org/divisions/III/members.html>. Membership of the Subcommittee on Photochemistry (2003–2005) was as follows: S. E. Braslavsky (Germany, Chairperson), A. U. Acuña (Spain), T. D. Z. Atvars (Brazil), C. Bohne (Canada), R. Bonneau (France), A. M. Braun (Germany), A. Chibisov (Russia), K. Ghiggino (Australia), A. Kutateladze (USA), H. Lemmetyinen (Finland), M. Litter (Argentina), H. Miyasaka (Japan), M. Olivucci (Italy), D. Phillips (UK), R. O. Rahn (USA), E. San Román (Argentina), N. Serpone (Canada), M. Terazima (Japan). Contributors to the 3rd edition were: A. U. Acuña, W. Adam, F. Amat, D. Armesto, T. D. Z. Atvars, A. Bard, E. Bill, L. O. Björn, C. Bohne, J. Bolton, R. Bonneau, H.