Binding affinity and equilibrium dissociation constant Kd
Answer to 1. Relationship between Affinity and Dissociation Constant Protein A has a binding site for ligand X with a Kd of M. Includes how KD correlates to antibody affinity and sensitivity, how KD values are measured and What is the relationship between KD and antibody affinity? Simultaneous Measurement of 10, Protein-Ligand Affinity Constants Using. Keywords: dissociation constant, protein interaction models, protein complex modelling, protein–protein docking, scoring functions, structure–affinity relations.
Comparison of Fetal and Maternal Hemoglobins Studies of oxygen transport in pregnant mammals show that the O2-saturation curves of fetal and maternal blood are markedly different when measured under the same conditions. Fetal erythrocytes contain a structural variant of hemoglobin, HbF, consisting of two a and two g subunits a2g2whereas maternal erythrocytes contain HbA a2b2. However, HbA now has a greater affinity for oxygen than does HbF. When BPG is reintroduced, the O2-saturation curves return to normal, as shown in the graph.
What is the effect of BPG on the O2 affinity of hemoglobin? How can the above information be used to explain the different O2 affinities of fetal and maternal hemoglobin? Thus, HbF must bind oxygen more tightly with higher affinity than HbA under physiological conditions. For maximal O2 transport, the oxygen pressure at which fetal blood approaches full saturation must be in the region where the O2 affinity of HbA is low.
This is indeed the case. Differential binding of BPG to the two hemoglobins may determine the difference in their O2 affinities. Hemoglobin Variants There are almost naturally occurring variants of hemoglobin.
Most are the result of a single amino acid substitution in a globin polypeptide chain. Some variants produce clinical illness, though not all variants have deleterious effects. A brief sample follows: Chapter 5 Protein Function S c The variant s most likely to show a decrease in BPG binding and an increase in the overall affinity of the hemoglobin for oxygen. Answer a Hb Memphis; it has a conservative substitution that is unlikely to have a significant effect on function.
The loss of an ion pair in Hb Cowtown may indicate loss of a charged residue, which would also change the pI, but there is not enough information to be sure. Oxygen Binding and Hemoglobin Structure A team of biochemists uses genetic engineering to modify the interface region between hemoglobin subunits. The resulting hemoglobin variants exist in solution primarily as dimers few, if any, 2 2 tetramers form. Are these variants likely to bind oxygen more weakly or more tightly? An inability to form tetramers would limit the cooperativity of these variants, and the binding curve would become more hyperbolic.
Also, the BPG-binding site would be disrupted. Oxygen binding would probably be tighter, because the default state in the absence of bound BPG is the tight-binding R state. At what concentration of antigen will v be a 0. For example, for a [L] 0. What does this tell you about the epitope recognized by the antibody?
Answer The epitope is likely to be a structure that is buried when G-actin polymerizes to form F-actin. The Immune System and Vaccines A host organism needs time, often days, to mount an immune response against a new antigen, but memory cells permit a rapid response to pathogens previously encountered.
A vaccine to protect against a particular viral infection often consists of weakened or killed virus or isolated proteins from a viral protein coat.
On subsequent infection, these cells can bind to the virus and trigger a rapid immune response. Some pathogens, including HIV, have developed mechanisms to evade the immune system, making it difficult or impossible to develop effective vaccines against them.
Lehninger Principles of Biochemistry 习题答案chapter 5_图文_百度文库
What strategy could a pathogen use to evade the immune system? Answer Many pathogens, including HIV, have evolved mechanisms by which they can repeatedly alter the surface proteins to which immune system components initially bind.
Thus the host organism regularly faces new antigens and requires time to mount an immune response to each one. As the immune system responds to one variant, new variants are created. S Chapter 5 Protein Function molecular mechanisms that are used to vary viral surface proteins are described in Part III of the text.
HIV uses an additional strategy to evade the immune system: Explain the molecular basis of the rigor state.
Answer Binding of ATP to myosin triggers dissociation of myosin from the actin thin filament. In the absence of ATP, actin and myosin bind tightly to each other. Sarcomeres from Another Point of View The symmetry of thick and thin filaments in a sarcomere is such that six thin filaments ordinarily surround each thick filament in a hexagonal array.
Dissociation constant - Wikipedia
Draw a cross section transverse cut of a myofibril at the following points: When the sarcomere contracts see Fig. Biochemistry on the Internet Lysozyme and Antibodies To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using Web-based protein databases and three-dimensional molecular viewing utilities.
Some molecular viewers require that you download a program or plug-in; some can be problematic when used with certain operating systems or browsers; some require the use of command-line code; some have a more user-friendly interface. We suggest you go to www. Choose the viewer most compatible with your operating system, browser, and level of expertise. Then download and install any software or plug-ins you may need. In this exercise you will examine the interactions between the enzyme lysozyme Chapter 4 and the Fab portion of the anti-lysozyme antibody.
To answer the following questions, use the information on the Structure Summary page at the Protein Data Bank www. Estimate the percentage of the lysozyme that interacts with the antigen-binding site of the antibody fragment. Are the residues contiguous in the primary sequence of the polypeptide chains?
Chain Y is lysozyme. Use the Jmol viewing utility at the PDB to view the complex. You should be able to identify the structures in the variable and constant regions of both the light and heavy chains.
The atoms will have asterisks when they are selected. A quick click on each atom will bring up identifying information. Repeat the process with each of the immunoglobulin chains selected to find the lysozyme residues at the interface. Not all these residues are adjacent in the primary structure. In any antibody, the residues in the VL and VH domains that come into contact with the antigen are located primarily in the loops connecting the b strands of the b-sandwich supersecondary structure.Affinity Constants
Folding of the polypeptide chain into higher levels of structure brings the nonconsecutive residues together to form the antigen-binding site. Exploring Reversible Interactions of Proteins and Ligands with Living Graphs Use the living graphs for Equations 5—8, 5—11, 5—14, and 5—16 to work through the following exercises.
For Equation 5—8, set up a plot of v versus [L] vertical and horizontal axes, respectively. Examine the plots generated when Kd is set at 5, 10, 20, and mM. Higher affinity of the protein for the ligand means more binding at lower ligand concentrations. Suppose that four different proteins exhibit these four different Kd values for ligand L. Which protein would have the highest affinity for L? Examine the plot generated when Kd 10 mM.
How much does v increase when [L] increases from 0. How much does v increase when [L] increases from 40 to 80 mM? You can do the same exercise for Equation 5— Convert [L] to pO2 and Kd to P Examine the curves generated when P50 is set at 0.
It is truly amazing that we are able to routinely characterize and understand protein folding, dynamics and interactions to such an extent and at such detailed resolution. How did we end up with such a vast amount of data for protein molecules?
Protein science is exactly years old, which translates into years of trying to understand the nature of protein molecules. While at Utrecht University, The Netherlands, Mulder described the chemical composition of fibrin, egg albumin and serum albumin [ 1 ], which was pioneering work that led to the initial and critical observation that distinct proteins are composed of the same chemical elements: Additionally, Mulder successfully characterized protein degradation products, such as leucine, determining an approximately correct molecular weight of the residue Da [ 2 ].
InFranz Hofmeister — and Emil Fischer —who spoke at a meeting in Karlsbad shortly after one another, independently announced that proteins are linear polymers consisting of amino acids linked by peptide bonds. The nature of the peptide bond in addition to the successful synthesis of the first optically active peptides by Otto Warburg in Fischer's laboratory were greatly influenced by the search for the 20 building blocks of proteins and prompted the investigation of the last few that were by that time still unknown: The primary structure of the proteins was finally elucidated inwhen Fred Sanger sequenced bovine insulin [ 6 ].
In the late s, John Kendrew determined the first crystal structure, that of sperm whale myoglobin [ 7 ], whereas Max Perutz determined the crystal structure of haemoglobin [ 8 ]. Interestingly, the crystal structure of haemoglobin is composed of four subunits, all non-covalently bound.
Such a quarternary structure did not come as a surprise, since Theodor Svedberg had already determined the molecular weight of haemoglobin and, therefore, its subunit composition in the mids [ 9 ].
Therefore, one should not forget that the discovery of the quaternary structure QS preceded the discovery of the primary [ 6 ], secondary [ 1011 ] and tertiary structures of proteins [ 78 ]. Whereas X-ray crystallography has proven to be the primary method for studying the atomic structure of biological macromolecules, nuclear magnetic resonance NMR spectroscopy allows both the three-dimensional structure and the dynamics of biomacromolecules to be probed.
Two years later, the first de novo NMR structure of a protein in solution was determined—that of the bull seminal protease inhibitor [ 13 ], reported the same year as the Lac repressor headpiece [ 14 ]. In the following years, structures of a plethora of biomacromolecules have been determined by X-ray crystallography and NMR and, as of Novemberapproximately 87 structures have been deposited in the public repository of macromolecular structures, the Protein Data Bank PDB database [ 1516 ].
- 1. Historical perspective
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Although the PDB already includes thousands of macromolecular complexes involved in protein—protein interactions, their importance in defining and orchestrating cellular processes was only recently appreciated [ 1718 ]. In the case of protein synthesis, it was known that macromolecular interactions must play a major role.
Still, DNA replication, transcription and translation were unexplored areas in biology at that time and up to now have been considered active areas of research. On the other hand, complete metabolic processes were characterized in detail, such as glycolysis [ 19 ], the Krebs cycle [ 20 ], cholesterol and fatty acid biosynthesis [ 21 ], which, again, erroneously led the community to believe that interactions were not essentially involved in the cellular metabolism.
Therefore, up to the s, macromolecular interactions were considered purification artefacts. For example, during the isolation and characterization of enzymes in vitro, several experimental difficulties arose as a result of protein—protein interactions, such as co-precipitation, which was believed to be contamination [ 23 ].
However, a unique observation back in by Frederic Richards gradually started to spark the interest in protein interaction phenomena [ 24 ]: