Reitmaier, Rick: Review of Immunoinformatic Approaches to In-silico B-Cell Epitope Prediction
... binding region. The hypervariable portions of the loops on the light chain are designated L1, L2 and L3 whilst those on the heavy chain are H1, H2, and H3. These regions are also known as complementary determining regions (CDRs) and this term is useful when discussing the general mechanism of bindin ...
... binding region. The hypervariable portions of the loops on the light chain are designated L1, L2 and L3 whilst those on the heavy chain are H1, H2, and H3. These regions are also known as complementary determining regions (CDRs) and this term is useful when discussing the general mechanism of bindin ...
Crossing borders to bind proteins—a new concept in protein
... According to this concept a fully assembled binder molecule consists of a small organic molecule or peptide that is linked with or without an interconnecting spacer to a 42-residue polypeptide selected from a set of only sixteen sequences (Fig. 1) [12]. The small molecule must bind to the protein bu ...
... According to this concept a fully assembled binder molecule consists of a small organic molecule or peptide that is linked with or without an interconnecting spacer to a 42-residue polypeptide selected from a set of only sixteen sequences (Fig. 1) [12]. The small molecule must bind to the protein bu ...
Exploring the Complement Interaction Network
... In a typical SPR experiment, one of the interaction partners (i.e. the ligand or target) is immobilized on the surface of a sensor chip, while the other partner (i.e. the analyte) is injected in solution (Fig. 1A). The sensor chip consists of a glass slide covered with a thin layer of gold. In order ...
... In a typical SPR experiment, one of the interaction partners (i.e. the ligand or target) is immobilized on the surface of a sensor chip, while the other partner (i.e. the analyte) is injected in solution (Fig. 1A). The sensor chip consists of a glass slide covered with a thin layer of gold. In order ...
Protein Engineering in the Development of
... residues lie in a plane along the length of a helix; the hydrophobic nature of the plane leads to the formation of multistranded coiled coils. The motif’s name reflects the predominance of leucine residues at the a and d positions. The aggregation or assembly of two or more domains into a coiled-coil ...
... residues lie in a plane along the length of a helix; the hydrophobic nature of the plane leads to the formation of multistranded coiled coils. The motif’s name reflects the predominance of leucine residues at the a and d positions. The aggregation or assembly of two or more domains into a coiled-coil ...
Localization of protein-binding sites within families of proteins
... We address the question of whether or not the positions of protein-binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein-binding sites are extra ...
... We address the question of whether or not the positions of protein-binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein-binding sites are extra ...
Identification of Plasmodium falciparum var1CSA
... the COS-7 cells showing bright surface fluorescence (Table 1, Fig. 1A). No IgM binding was detected with any of the other domains including the highly expressed domain DBL5␥ (Table 1, Fig. 1B). Identical results were obtained with an affinity-purified goat polyclonal anti-human IgM reagent (Rockland ...
... the COS-7 cells showing bright surface fluorescence (Table 1, Fig. 1A). No IgM binding was detected with any of the other domains including the highly expressed domain DBL5␥ (Table 1, Fig. 1B). Identical results were obtained with an affinity-purified goat polyclonal anti-human IgM reagent (Rockland ...
Structure/activity studies of anti-inflammatory
... amino acid substitutions are tolerated in the peptide without complete loss of inhibitory activity, substitution at some positions (e.g., the W residue) results in relatively inactive compounds, clearly pointing to the importance of these residues in making critical contacts with the appropriate sac ...
... amino acid substitutions are tolerated in the peptide without complete loss of inhibitory activity, substitution at some positions (e.g., the W residue) results in relatively inactive compounds, clearly pointing to the importance of these residues in making critical contacts with the appropriate sac ...
Affinity Chromatography
... In this seminal paper, the general principles and potential application of affinity chromatography were enunciated and have largely remained unchanged until the present date. The paper contained several important contributions. First, it generalized the technique to all potential enzyme purification ...
... In this seminal paper, the general principles and potential application of affinity chromatography were enunciated and have largely remained unchanged until the present date. The paper contained several important contributions. First, it generalized the technique to all potential enzyme purification ...
Enzymes - CSUN Moodle
... – Mass balance equation for enzyme: ETot = [E] + [ES] – It is also implicitly assumed that: STot = [S] + [ES] ≈ [S] ...
... – Mass balance equation for enzyme: ETot = [E] + [ES] – It is also implicitly assumed that: STot = [S] + [ES] ≈ [S] ...
Docking with GOLD Tutorial
... Configuration File User Guide at https://www.ccdc.cam.ac.uk/support-andresources/ccdcresources/gold_conf.pdf for more information. The GOLD configuration file specifies the location of: a. the prepared 3D coordinates of your ligand b. the prepared 3D coordinates of your protein An example of a prepa ...
... Configuration File User Guide at https://www.ccdc.cam.ac.uk/support-andresources/ccdcresources/gold_conf.pdf for more information. The GOLD configuration file specifies the location of: a. the prepared 3D coordinates of your ligand b. the prepared 3D coordinates of your protein An example of a prepa ...
Topic: Developmental biology Extra
... The Atp6v0a4-null line, in which a LacZ reporter cassette replaced part of the gene, was used to study novel locations of the a4 subunit. Initially, using β-galactosidase as a reporter for the null gene, a4 expression was investigated in a range of tissues and RT-PCR was used to detect the expressio ...
... The Atp6v0a4-null line, in which a LacZ reporter cassette replaced part of the gene, was used to study novel locations of the a4 subunit. Initially, using β-galactosidase as a reporter for the null gene, a4 expression was investigated in a range of tissues and RT-PCR was used to detect the expressio ...
Voet Chapter 12 Slides
... (gel, membrane) is exposed to X-ray film, dark staining, replaced by phosphorimagers Microradiography, cover sample with photographic emulsion and examining under microscope ...
... (gel, membrane) is exposed to X-ray film, dark staining, replaced by phosphorimagers Microradiography, cover sample with photographic emulsion and examining under microscope ...
127 - Chimica
... Summary: The reaction of [Re,(CO),,] with OH- gives first [Re,H(CO),]- and then, under more drastic conditions, the novel anion [Re2H,(CO),I2-, which can be reversibly protonated to give [ Re,H,(p-H)(CO),]-, whose structure has been elucidated by a X-ray investigation. Variable-temperature NMR spect ...
... Summary: The reaction of [Re,(CO),,] with OH- gives first [Re,H(CO),]- and then, under more drastic conditions, the novel anion [Re2H,(CO),I2-, which can be reversibly protonated to give [ Re,H,(p-H)(CO),]-, whose structure has been elucidated by a X-ray investigation. Variable-temperature NMR spect ...
A Molecular Model of Agonist and Nonpeptide Antagonist Binding to
... increase in the affinity toward OPC-21268. To gain information about the location of the OPC-21268 binding site, a model of this compound was docked onto a homology-built three-dimensional model of the human V1R. The hydrophobic moieties of this nonpeptide antagonist were found to be located deep wi ...
... increase in the affinity toward OPC-21268. To gain information about the location of the OPC-21268 binding site, a model of this compound was docked onto a homology-built three-dimensional model of the human V1R. The hydrophobic moieties of this nonpeptide antagonist were found to be located deep wi ...
Six Distinct Nuclear Factors Interact with the 75-Base
... With this methodology, we found that WEHI 231 nuclear proteins bind to a number of sites within the Mo-MuLV enhancer. This became clear when fragment I was used because a multiplicity of protein-DNA complexes was observed (Fig. 2, lane 1). These bands could be partially resolved by chromatographical ...
... With this methodology, we found that WEHI 231 nuclear proteins bind to a number of sites within the Mo-MuLV enhancer. This became clear when fragment I was used because a multiplicity of protein-DNA complexes was observed (Fig. 2, lane 1). These bands could be partially resolved by chromatographical ...
Team Publications
... motility of the motor. It is thought that each head of a two-headed myosin VI molecule binds one calmodulin (CaM) by means of a single “IQ motif”. Using truncations of the myosin VI protein and electrospray ionization(ESI)-MS, we demonstrate that in fact each myosin VI head binds two CaMs. One CaM b ...
... motility of the motor. It is thought that each head of a two-headed myosin VI molecule binds one calmodulin (CaM) by means of a single “IQ motif”. Using truncations of the myosin VI protein and electrospray ionization(ESI)-MS, we demonstrate that in fact each myosin VI head binds two CaMs. One CaM b ...
Transcription Factor Veracity: 1s GBF3 Responsible for ABA
... Assignment of particular transcription factors to specific roles in promoter elements can be problematic, especially i n systems such as the G-box, where multiple factors of overlapping specificity exist. In the Arabidopsis alcohol dehydfogenase (Adh) promoter, the G-box regulates expression in resp ...
... Assignment of particular transcription factors to specific roles in promoter elements can be problematic, especially i n systems such as the G-box, where multiple factors of overlapping specificity exist. In the Arabidopsis alcohol dehydfogenase (Adh) promoter, the G-box regulates expression in resp ...
Gmelin Tips and Reminders
... • Linearized Structure Formula: LSF: a linear representation of a compound’s structure. This can include isotopes. Compounds can consist of more than one fragment being separated in the linearized structure formula field by an asterisk (*); formulas within systems are separated by a hush mark (#); d ...
... • Linearized Structure Formula: LSF: a linear representation of a compound’s structure. This can include isotopes. Compounds can consist of more than one fragment being separated in the linearized structure formula field by an asterisk (*); formulas within systems are separated by a hush mark (#); d ...
Complexation Reactions
... Palladium(II) tends to form complexes with coordination number 4. A compound has the composition PdCl2 · 3 NH3. (a) Write the formula for this compound that best shows the coordination structure. (b) When an aqueous solution of the compound is treated with excess AgNO3(aq), how many moles of AgCl(s) ...
... Palladium(II) tends to form complexes with coordination number 4. A compound has the composition PdCl2 · 3 NH3. (a) Write the formula for this compound that best shows the coordination structure. (b) When an aqueous solution of the compound is treated with excess AgNO3(aq), how many moles of AgCl(s) ...
The Behavior of Proteins: Enzymes, Mechanisms
... Grants as implemented by the U.S. Department of Labor’s Employment and Training Administration. The solution was created by the grantee and does not necessarily reflect the official position of the U.S. Department of Labor. The Department of Labor makes no guarantees, warranties, or assurances of an ...
... Grants as implemented by the U.S. Department of Labor’s Employment and Training Administration. The solution was created by the grantee and does not necessarily reflect the official position of the U.S. Department of Labor. The Department of Labor makes no guarantees, warranties, or assurances of an ...
Monoclonal Antibodies - Kenan Fellows Program
... Scatchard plot analysis Scatchard plots are based on repeated equilibrium dialyses with a constant concentration of antibody and varying concentration of ligand. In these plots, r = moles bound ligand/mole antibody and c = free ligand. From a Scatchard plot, both the equilibrium constant (K) and th ...
... Scatchard plot analysis Scatchard plots are based on repeated equilibrium dialyses with a constant concentration of antibody and varying concentration of ligand. In these plots, r = moles bound ligand/mole antibody and c = free ligand. From a Scatchard plot, both the equilibrium constant (K) and th ...
Recognition of complex carbohydrates by the macrophage mannose
... Since CRD 4 was the only domain found to show carbohydrate-binding activity in the absence of other CRDs, this domain was produced in a bacterial expression system so that its binding properties could be characterized further [ 161. Correctly folded CRI) 4 was purified from the bacteria by affinity ...
... Since CRD 4 was the only domain found to show carbohydrate-binding activity in the absence of other CRDs, this domain was produced in a bacterial expression system so that its binding properties could be characterized further [ 161. Correctly folded CRI) 4 was purified from the bacteria by affinity ...
Poster
... β-catenin is a multi-functional protein involved in two essential cellular pathways: cell-cell adhesion and transcriptional regulation8. β-catenin contains 12 armadillo repeats capped by a C-helix. An amino acid important for β-catenin’s electrostatic interactions with ligands is Lys-435 known as th ...
... β-catenin is a multi-functional protein involved in two essential cellular pathways: cell-cell adhesion and transcriptional regulation8. β-catenin contains 12 armadillo repeats capped by a C-helix. An amino acid important for β-catenin’s electrostatic interactions with ligands is Lys-435 known as th ...
Enzymes: Principles of Catalysis
... • Carry out algebra ... – ... or graph theory for complex reactions • Simplest Model Mechanism: E + S ES E + P – One reactant, one product, no inhibitors ...
... • Carry out algebra ... – ... or graph theory for complex reactions • Simplest Model Mechanism: E + S ES E + P – One reactant, one product, no inhibitors ...
9th Lecture Updated
... antibacterial agents called oxazolidinones It is the first commercially available oxazolidinone antibiotic and the only marketed oxazolidinone, although others are in development ...
... antibacterial agents called oxazolidinones It is the first commercially available oxazolidinone antibiotic and the only marketed oxazolidinone, although others are in development ...
Cooperative binding
Molecular binding is an interaction between molecules that results in a stable physical association between those molecules. Cooperative binding occurs in binding systems that are constituted by more than one type (species) of molecule (say molecules A and B) and in which one of the partners is not mono-valent; i.e., it binds more than one molecule of the other molecular species. For example, one molecule of type A can bind 6 molecules of type B (in such cases, B is usually referred to as the ""ligand""). Binding in this type of system can be considered ""cooperative"" if the binding of B to one site on A is affected by the binding of B to other site(s) on A. In other words, the binding of B molecules to the different sites on A do not constitute mutually independent events. This can be due, for instance, to an affinity for the ligand that depends on the amount of ligand bound. Cooperativity can be positive or negative. Cooperative binding is observed in many biopolymers, including proteins and nucleic acids. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes.