Hemoglobin
... non-polar groups (methyls and vinyls, (see above, Fig. 1) on the porphyrin rings in this pocket and the two propanoate groups on the exterior (see above, Fig. 4, the red balls represent the O atoms in the -CH2CH2CO2- groups). In addition to these non-covalent interactions, the heme unit is bound cov ...
... non-polar groups (methyls and vinyls, (see above, Fig. 1) on the porphyrin rings in this pocket and the two propanoate groups on the exterior (see above, Fig. 4, the red balls represent the O atoms in the -CH2CH2CO2- groups). In addition to these non-covalent interactions, the heme unit is bound cov ...
In Silico Analysis of Mytilus Galloprovincialis Proximal Thread Matrix
... 4CN8. Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other. When the protein binds with the ligand, there is some energy released which is called binding energy and it is represented by E-value. This value helps to know the strength of bin ...
... 4CN8. Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other. When the protein binds with the ligand, there is some energy released which is called binding energy and it is represented by E-value. This value helps to know the strength of bin ...
A survey of conformational and energetic changes in G protein
... G protein-coupled receptors (GPCRs) are the largest and most diverse class of membrane receptors in eukaryotes [1]; they bind many different types of ligands to initiate an array of intracellular signaling cascades. GPCRs primarily interact with membrane associated, heterotrimeric complexes called G ...
... G protein-coupled receptors (GPCRs) are the largest and most diverse class of membrane receptors in eukaryotes [1]; they bind many different types of ligands to initiate an array of intracellular signaling cascades. GPCRs primarily interact with membrane associated, heterotrimeric complexes called G ...
Bio9A Quiz 1 Study Guide
... c. Endocytosis – particles are taken in. (Fig 5.15) i. Phagocytosis – large particles are taken in – “cell eating”. Vacuole is formed which may fuse with a lysosome. ii. Pinocytosis – small particles are ingested – “cell drinking”.Vesicle then allows contents to bleed into cytosol. iii. Receptor-med ...
... c. Endocytosis – particles are taken in. (Fig 5.15) i. Phagocytosis – large particles are taken in – “cell eating”. Vacuole is formed which may fuse with a lysosome. ii. Pinocytosis – small particles are ingested – “cell drinking”.Vesicle then allows contents to bleed into cytosol. iii. Receptor-med ...
Molecular and General Genetics
... through PhoE protein pores. Thus, by exchanging amino acid residues 2-73 of PhoE protein by the homologous part of OmpF protein, the pores lose part of their anion specificity. Phage receptor activity PhoE protein serves as (part of) the receptor for phage TC45 and its host range derivative TC45hrN3 ...
... through PhoE protein pores. Thus, by exchanging amino acid residues 2-73 of PhoE protein by the homologous part of OmpF protein, the pores lose part of their anion specificity. Phage receptor activity PhoE protein serves as (part of) the receptor for phage TC45 and its host range derivative TC45hrN3 ...
(a) (c)
... • Commonly act as hormones that will “turn on” or “turn off” genes. • Are made of four fused carbon rings and differ mostly because of their “attachments” (side branches) • Can travel right through the cell membrane as they are non-polar. ...
... • Commonly act as hormones that will “turn on” or “turn off” genes. • Are made of four fused carbon rings and differ mostly because of their “attachments” (side branches) • Can travel right through the cell membrane as they are non-polar. ...
The variable and conserved interfaces of modeled olfactory receptor
... Fig. 1. Multiple alignment of OR proteins ~upper rows! and non-OR GPCRs ~lower rows!. Five typical OR sequences and five non-OR sequences are shown. The row marked “OR Cons” is the consensus of all 197 OR sequences analyzed in this study, calculated by 65% plurality. The OR sequences shown are: 17–2 ...
... Fig. 1. Multiple alignment of OR proteins ~upper rows! and non-OR GPCRs ~lower rows!. Five typical OR sequences and five non-OR sequences are shown. The row marked “OR Cons” is the consensus of all 197 OR sequences analyzed in this study, calculated by 65% plurality. The OR sequences shown are: 17–2 ...
revised
... Using the TMHMM program, a total of 21473 TMs for the mesophilic set of proteins and 13340 for the thermophilic organims were predicted. The average length of the predicted TMs was 22 for both sets of proteins (thermophilic and mesophilic), which is in good agreement with the average length of TMs p ...
... Using the TMHMM program, a total of 21473 TMs for the mesophilic set of proteins and 13340 for the thermophilic organims were predicted. The average length of the predicted TMs was 22 for both sets of proteins (thermophilic and mesophilic), which is in good agreement with the average length of TMs p ...
Structural diversity of band 4.1 superfamily members
... belongs to the band 4.1 superfamily (Rees et al., 1990). Talin is a protein with a molecular mass of ~200 kDa, which is concentrated at the undercoat of cell-to-substrate adherens junctions (focal contacts) (Burridge and Connell, 1983; Burridge and Mangeat, 1984). This protein is thought to play an ...
... belongs to the band 4.1 superfamily (Rees et al., 1990). Talin is a protein with a molecular mass of ~200 kDa, which is concentrated at the undercoat of cell-to-substrate adherens junctions (focal contacts) (Burridge and Connell, 1983; Burridge and Mangeat, 1984). This protein is thought to play an ...
Structural Basis of Wnt Recognition by Frizzled
... XWnt8 has an unusual two-domain structure (Figure 2), and each domain extends a betastrand or ‘finger’, which ‘grasps’ the Fz8-CRD on opposite faces. Site 1 interaction is primarily mediated by a palmitoleic acid covalently attached to a conserved Serine at the tip of ‘thumb’, which binds within a ...
... XWnt8 has an unusual two-domain structure (Figure 2), and each domain extends a betastrand or ‘finger’, which ‘grasps’ the Fz8-CRD on opposite faces. Site 1 interaction is primarily mediated by a palmitoleic acid covalently attached to a conserved Serine at the tip of ‘thumb’, which binds within a ...
Pseudoatom-driven solvent accessibility refinement (PaDSAR) Method
... Patching and solvating the full-length models with pseudoatoms Two categories of pseudoatoms are introduced in the system, i.e., spin-label pseudoatoms and environment pseudoatoms [1], as summarized in Table 1. The spin-label pseudoatoms are further classified into five different types, denoted EP1, ...
... Patching and solvating the full-length models with pseudoatoms Two categories of pseudoatoms are introduced in the system, i.e., spin-label pseudoatoms and environment pseudoatoms [1], as summarized in Table 1. The spin-label pseudoatoms are further classified into five different types, denoted EP1, ...
EMBO EMBO EMBO
... (Figure 1C), an iodobenzyl derivative of the potent inhibitor 2-PMPA, was determined by single-wavelength anomalous dispersion (SAD), making use of the zinc ions at the catalytic center of the enzyme, along with a strong contribution from the iodine atom present in the inhibitor (see Supplementary T ...
... (Figure 1C), an iodobenzyl derivative of the potent inhibitor 2-PMPA, was determined by single-wavelength anomalous dispersion (SAD), making use of the zinc ions at the catalytic center of the enzyme, along with a strong contribution from the iodine atom present in the inhibitor (see Supplementary T ...
... recognition. Omithodorin, a thrombin inhibitor from the tick O. moubala has been cocrystallized with thrombin (van de Locht, 1996). It consist of aN-terminal BPTI-Iike domain (I '-53 ' ) and a C-terminal BPTI-Iike domain (60 '-119 ') connected by 7 amino acid residues. The N-terminal domain is invol ...
Lipoproteins
... A domain subject to O-linked glysosylation (GD), between the innermost EGF domain & the transmembrane a-helix, may act as a spacer to extend the LDL-binding region out from the cell surface. ...
... A domain subject to O-linked glysosylation (GD), between the innermost EGF domain & the transmembrane a-helix, may act as a spacer to extend the LDL-binding region out from the cell surface. ...
... usually co-expressed with anti-sigma factors that bind to and sequester the sigma factor to keep it in an inactive state (Staroń et al., 2009; Bastiaansen et al., 2012). In Gramnegative bacteria, these anti-sigma factors are typically cytoplasmic membrane proteins that contain a short cytosolic N-te ...
The Plant Cell
... protein (924 amino acids) was obtained from GenBank (Table 1). It consists of three putative SH3 binding PRDs and a C-terminal DnaJ domain (Figure 8B). Sequence alignment suggested that the DnaJ domain was similar only to those from the auxilin protein family (Figure 8C). Significantly, the plant Dn ...
... protein (924 amino acids) was obtained from GenBank (Table 1). It consists of three putative SH3 binding PRDs and a C-terminal DnaJ domain (Figure 8B). Sequence alignment suggested that the DnaJ domain was similar only to those from the auxilin protein family (Figure 8C). Significantly, the plant Dn ...
EF-Tu PROTEIN DOMAINS
... The bacterial elongation factor Tu (EF-Tu) has been extensively studied for decades as it plays a key role in protein biosynthesis. It is a model, multifunctional GTP-protein. This protein is also in the centre of interest as a possible target for new antibiotics. Moreover, the high homology in stru ...
... The bacterial elongation factor Tu (EF-Tu) has been extensively studied for decades as it plays a key role in protein biosynthesis. It is a model, multifunctional GTP-protein. This protein is also in the centre of interest as a possible target for new antibiotics. Moreover, the high homology in stru ...
HOMOLOGY MODELING OF ARYL HYDROCARBON RECEPTOR AND DOCKING OF AGONISTS
... the antagonists, both flavonoids and nonflavonoids form H-bonds with the amino acid residues on the AhR which include His-285, Ser340, Thr-343 and Thr-283. The flavonoids formed H-bonds with the receptor mainly via groups present on the 3’ and 4’ position of the Bring. Highest activity was reported ...
... the antagonists, both flavonoids and nonflavonoids form H-bonds with the amino acid residues on the AhR which include His-285, Ser340, Thr-343 and Thr-283. The flavonoids formed H-bonds with the receptor mainly via groups present on the 3’ and 4’ position of the Bring. Highest activity was reported ...
The outer membrane of Borrelia
... Borrelia burgdorferi protein BBK32 binds to soluble fibronectin via the Nterminal 70 kDa region, causing fibronectin to undergo conformational extension Gemma Harris, W. Ma, LM, Maurer, JR. Potts and DF.Mosher, J. ...
... Borrelia burgdorferi protein BBK32 binds to soluble fibronectin via the Nterminal 70 kDa region, causing fibronectin to undergo conformational extension Gemma Harris, W. Ma, LM, Maurer, JR. Potts and DF.Mosher, J. ...
An ATPase domain common to prokaryotic cell cycle proteins, sugar
... of the three structures and alignment of many sequences in each of the three families has revealed a set of common conserved residues, distributed in five sequence motifs, which are involved in ATP binding and in a putative interdomain hinge. From the multiple sequence aliment in these motifs a patt ...
... of the three structures and alignment of many sequences in each of the three families has revealed a set of common conserved residues, distributed in five sequence motifs, which are involved in ATP binding and in a putative interdomain hinge. From the multiple sequence aliment in these motifs a patt ...
Chapter 12: Protein structure, stability and folding
... pathways. Many proteins which have been isolated and then completely unfolded, can be induced to rapidly and spontaneously refold to form the proper 3-dimensional structure ...
... pathways. Many proteins which have been isolated and then completely unfolded, can be induced to rapidly and spontaneously refold to form the proper 3-dimensional structure ...
440-kD Ankyrins: Structure of the Major
... number corresponding to the entire 440-kD ankyrins. These sequence data are available from EMBL/Genbank/DDBJ under accession number Z26634. ...
... number corresponding to the entire 440-kD ankyrins. These sequence data are available from EMBL/Genbank/DDBJ under accession number Z26634. ...
Full Text
... 42%, while the sequence identity in the same region is 9.5%. Only one gap in the conserved helical regions required closing during the threading process. The initial automatic alignment revealed three residues known to be involved in anesthetic binding at the same relative height along the core axis ...
... 42%, while the sequence identity in the same region is 9.5%. Only one gap in the conserved helical regions required closing during the threading process. The initial automatic alignment revealed three residues known to be involved in anesthetic binding at the same relative height along the core axis ...
The Nterminal region of the bacterial DNA polymerase PolC features
... 230 residues, both the structure and function are unknown. In the present study, using sensitive homology detection and comparative protein structure modeling, we identified, in this enigmatic region, two consecutive globular domains, PolC-NI and PolC-NII, which are followed by an apparently unstru ...
... 230 residues, both the structure and function are unknown. In the present study, using sensitive homology detection and comparative protein structure modeling, we identified, in this enigmatic region, two consecutive globular domains, PolC-NI and PolC-NII, which are followed by an apparently unstru ...
Test 1 Study Guide
... iv. Phagocytosis – large particles are taken in by membrane invagination. Uses lots of ATP (Fig. 5.18) v. Endocytosis – smaller particles taken into a vesicle. (Fig. 5.19) 1. Receptor mediated endocytosis. Meant for specific molecules (ligands). Receptors are organized on surface by clathrin. Once r ...
... iv. Phagocytosis – large particles are taken in by membrane invagination. Uses lots of ATP (Fig. 5.18) v. Endocytosis – smaller particles taken into a vesicle. (Fig. 5.19) 1. Receptor mediated endocytosis. Meant for specific molecules (ligands). Receptors are organized on surface by clathrin. Once r ...
Anthrax toxin
Anthrax toxin is a three-protein exotoxin secreted by virulent strains of the bacterium, Bacillus anthracis—the causative agent of anthrax. The toxin was first discovered by Harry Smith in 1954. Anthrax toxin is composed of a cell-binding protein, known as protective antigen (PA), and two enzyme components, called edema factor (EF) and lethal factor (LF). These three protein components act together to impart their physiological effects. Assembled complexes containing the toxin components are endocytosed. In the endosome, the enzymatic components of the toxin translocate into the cytoplasm of a target cell. Once in the cytosol, the enzymatic components of the toxin disrupts various immune cell functions, namely cellular signaling and cell migration. The toxin may even induce cell lysis, as is observed for macrophage cells. Anthrax toxin allows the bacteria to evade the immune system, proliferate, and ultimately kill the host animal. Research on anthrax toxin also provides insight into the generation of macromolecular assemblies, and on protein translocation, pore formation, endocytosis, and other biochemical processes.