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pdf file - John Innes Centre
pdf file - John Innes Centre

... complex has a stoichiometry of 1:1, and all molecules of GlnK within the complex are fully deuridylylated (15). The crystal structure of the AmtB-GlnK complex revealed that ADP and not ATP is present in all three lateral clefts of GlnK and that 2-OG and Mg2⫹ ions are absent (23, 25). The conformatio ...
Problem 28. TUNNELING IN CHEMISTRY
Problem 28. TUNNELING IN CHEMISTRY

... In chemical reactions molecular structure changes over time so that the electronic state of a molecule is a function of time. In some cases structure of a molecule can be presented by a superposition of the initial and final states with time-dependent coefficients. Let’s assume that a molecule oscil ...
STOICHIOMETRY via ChemLog - Small
STOICHIOMETRY via ChemLog - Small

... When carrying out a chemical reaction, we may use the exact amount of each reactant needed. Or, we may use an excess of some reactants and a limited amount of others. We may do this if one reactant is very expensive and others are inexpensive so that we can use all of the expensive compound. It can ...
Math for Biology - An Introduction
Math for Biology - An Introduction

... We will NOT be solving differential equations The tools - Rule Bender and BioNetGen - will do that for us This lecture is designed to give some background about what the programs are doing ...
All-Atom Molecular Dynamics of Virus Capsids
All-Atom Molecular Dynamics of Virus Capsids

... and molecular dynamics flexible fitting (MDFF).25 Conical capsids, such as HIV-1, lack overall symmetry, which poses a tremendous challenge to resolving their chemical structure. In these cases, MDFF25 can be essential to obtaining all-atom models. For example, the structure of the helical lattice of ...
Ligand Binding and Allosteric Regulation
Ligand Binding and Allosteric Regulation

... – Amino acid differences between  and  reduces HbF's affinity for 2,3-BPG, thus increasing its affinity for O2 under physiological conditions. ...
Renin Precursor Synthesis and Renin
Renin Precursor Synthesis and Renin

... Proteins are synthesized in the cytoplasma of the cell by the ribosomes, which use RNA as a messenger for the amino acid sequence. Ribosomes from one species and messenger RNA from another can interact and produce a protein with the correct structure. This is used in the so-called cellfree translati ...
Revised (12 Sept 2009)  Topic: Chemical Equilibrium
Revised (12 Sept 2009) Topic: Chemical Equilibrium

... This indicates that the concentration of Fe(NCS)2+(aq) is bigger than its concentration at equilibrium and the reversible reaction is not at equilibrium. In order to reach equilibrium, the value must be restored to 138. This can be achieved if some Fe(NCS)2+(aq) ions react (making the numerator smal ...
CHAPTER 6
CHAPTER 6

... • Lactate is then returned to the liver, where it can be reoxidized to pyruvate by liver LDH • Liver provides glucose to muscle for exercise and then reprocesses lactate into new glucose ...
Rabbit Reticulocyte Lysate Technical Manual
Rabbit Reticulocyte Lysate Technical Manual

... purified to remove contaminating cells. The packed cells then are lysed by the addition of water. Untreated Rabbit Reticulocyte Lysate is provided in 1ml aliquots. Note: Untreated Rabbit Reticulocyte Lysate is not supplemented with tRNA, creatine phosphate, creatine phosphokinase, DTT, potassium ace ...
Document
Document

... protein chemistry to suit the use of the machine. 2. works in a problem-oriented manner in which experience and knowledge are adopted to accommodate available machines. 3. relies first on imagination, then knowledge, then machines (Consider the contrast between H. Noyrath vrs. B. Hartley). What was ...
Chapter 7 - NordoniaHonorsChemistry
Chapter 7 - NordoniaHonorsChemistry

... Tro's "Introductory Chemistry", Chapter 7 ...
The Vps13p–Cdc31p complex is directly required for TGN late
The Vps13p–Cdc31p complex is directly required for TGN late

Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose
Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose

... It is clear that phosphate is required for the continued operation of glycolysis and ethanol formation. In extracts to which glucose is added, fermentation proceeds until ADP and Pi (present in the extracts) are exhausted. (a) Phosphate is required in the glyceraldehyde 3-phosphate dehydrogenase rea ...
world journal of pharmaceutical research
world journal of pharmaceutical research

Feeney_ku_0099D_12934_DATA_1 - KU ScholarWorks
Feeney_ku_0099D_12934_DATA_1 - KU ScholarWorks

... ii ...
20. Chemical Equilibrium
20. Chemical Equilibrium

... are converted to products before a reaction stops. In truth, however, experiments show that the conversion of reactants into products is often incomplete in chemical reactions. This is the case no matter how long the reaction is allowed to continue. As a reaction progresses, the concentrations of th ...
Chapter 19
Chapter 19

... Determining Oxidation Numbers In order to understand all types of redox reactions, you must have a way to determine the oxidation number (n element) of the atoms involved in the reaction. Table 19.2 outlines the rules chemists use to make this determination easier. Many elements other than those sp ...
The Chemistry and Evolution of Enzyme Function
The Chemistry and Evolution of Enzyme Function

... member of such great academic institutions. Friends mean freedom. To Anna, Bruno and Claire for sharing my passion for cooking and being an unlimited source of social gatherings and walks alongside Paradise. To Matthias, Ulla and Nidhi for your everlasting bad jokes (see beginning and end of Acknowl ...
Some Structural and Kinetic Aspects of L
Some Structural and Kinetic Aspects of L

... from a single gene by use of different promoters. The R type pyruvate kinase subunit is larger about 3500 Da then L type and it is proposed that it has an additional peptide located in N-terminal end of enzyme subunit. The L type is the only one isoenzyme of these four types, which can be regulated ...
Topic 3: Chemical Kinetics - Manitoba Education and Training
Topic 3: Chemical Kinetics - Manitoba Education and Training

... Demonstrate appropriate scientific skills when seeking answers to questions. Demonstrate curiosity, skepticism, creativity, open-mindedness, accuracy, precision, honesty, and persistence, and appreciate their importance as scientific and technological habits of mind. Understand the properties and st ...
The rotary mechanism of the ATP synthase Archives - iGRAD
The rotary mechanism of the ATP synthase Archives - iGRAD

... and the F1 d subunit. At least on a gross level, we finally understood the role of each subunit in the complex. Because of the large size, multiple subunits many of which are integral membrane proteins, and asymmetry, determination of the subunit stoichiometry and defining subunit interactions has bee ...
Chemical Equilibria - Beck-Shop
Chemical Equilibria - Beck-Shop

... Q: Why are the terms involving solids and liquids not included in the equilibrium constant expression for heterogeneous equilibrium? A: For a given temperature, the saturated vapour pressures of solids (and that of liquids) are constant. In addition, even though their actual amounts may change, both ...
Exploring the Complement Interaction Network
Exploring the Complement Interaction Network

[7] Semisynthesis of Proteins Containing Selenocysteine
[7] Semisynthesis of Proteins Containing Selenocysteine

... A p-methoxybenzyl (PMB) group is used to protect the selenium, according to the examples of Koide et al. 18 and Besse and Moroder. 19 The following procedure was adapted from Koide et al. 18 Their procedure uses an excess of p-methoxybenzyl chloride in the reaction under highly basic conditions. In ...
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Multi-state modeling of biomolecules

Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour of biological molecules or complexes that can adopt a large number of possible functional states.Biological signaling systems often rely on complexes of biological macromolecules that can undergo several functionally significant modifications that are mutually compatible. Thus, they can exist in a very large number of functionally different states. Modeling such multi-state systems poses two problems: The problem of how to describe and specify a multi-state system (the ""specification problem"") and the problem of how to use a computer to simulate the progress of the system over time (the ""computation problem""). To address the specification problem, modelers have in recent years moved away from explicit specification of all possible states, and towards rule-based formalisms that allow for implicit model specification, including the κ-calculus, BioNetGen, the Allosteric Network Compiler and others. To tackle the computation problem, they have turned to particle-based methods that have in many cases proved more computationally efficient than population-based methods based on ordinary differential equations, partial differential equations, or the Gillespie stochastic simulation algorithm. Given current computing technology, particle-based methods are sometimes the only possible option. Particle-based simulators further fall into two categories: Non-spatial simulators such as StochSim, DYNSTOC, RuleMonkey, and NFSim and spatial simulators, including Meredys, SRSim and MCell. Modelers can thus choose from a variety of tools; the best choice depending on the particular problem. Development of faster and more powerful methods is ongoing, promising the ability to simulate ever more complex signaling processes in the future.
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