Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily

Surfactant protein (SP) A and SP-D are collagenous glycoproteins with multiple functions in the lung. Both of these proteins are calcium-dependent lectins and are structurally similar to mannose-binding protein and bovine conglutinin. Both form polyvalent multimeric structures for interactions with pathogens, cells, or other molecules. SP-A is an integral part of the surfactant system, binds phospholipids avidly, and is found in lamellar bodies and tubular myelin. Initially, most research interest focused on its role in surfactant homeostasis. Recently, more attention has been placed on the role of SP-A as a host defense molecule and its interactions with pathogens and phagocytic cells. SP-D is much less involved with the surfactant system. SP-D appears to be primarily a host defense molecule that binds surfactant phospholipids poorly and is not found in lamellar inclusion bodies or tubular myelin. Both SP-A and SP-D bind a wide spectrum of pathogens including viruses, bacteria, fungi, and pneumocystis. In addition, both molecules have been measured in the systemic circulation by immunologic methods and may be useful biomarkers of disease. The current challenges are characterization of the three-dimensional crystal structure of SP-A and SP-D, molecular cloning of their receptors, and determination of their precise physiological functions in vivo.

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Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase

Biochemical Journal ◽

10.1042/bj20051374 ◽

2005 ◽

Vol 393 (2) ◽

pp. 503-511 ◽

Cited By ~ 71

Author(s):

Sergey A. Shiryaev ◽

Boris I. Ratnikov ◽

Alexei V. Chekanov ◽

Sergey Sikora ◽

Dmitri V. Rozanov ◽

...

Keyword(s):

West Nile Virus ◽

Protein A ◽

Three Dimensional ◽

Proteolytic Processing ◽

Three Dimensional Model ◽

West Nile ◽

Highly Active ◽

Polyprotein Precursor ◽

Global Threat

Mosquito-borne WNV (West Nile virus) is an emerging global threat. The NS3 proteinase, which is essential for the proteolytic processing of the viral polyprotein precursor, is a promising drug target. We have isolated and biochemically characterized the recombinant, highly active NS3 proteinase. We have determined that the NS3 proteinase functions in a manner that is distantly similar to furin in cleaving the peptide and protein substrates. We determined that aprotinin and D-arginine-based 9–12-mer peptides are potent inhibitors of WNV NS3 with Ki values of 26 nM and 1 nM respectively. Consistent with the essential role of NS3 activity in the life cycle of WNV and with the sensitivity of NS3 activity to the D-arginine-based peptides, we showed that nona-D-Arg-NH2 reduced WNV infection in primary neurons. We have also shown that myelin basic protein, a deficiency of which is linked to neurological abnormalities of the brain, is sensitive to NS3 proteolysis in vitro and therefore this protein represents a convenient test substrate for the studies of NS3. A three-dimensional model of WNV NS3 that we created may provide a structural guidance and a rationale for the subsequent design of fine-tuned inhibitors. Overall, our findings represent a foundation for in-depth mechanistic and structural studies as well as for the design of novel and efficient inhibitors of WNV NS3.

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Three-dimensional localization of CENP-A suggests a complex higher order structure of centromeric chromatin

The Journal of Cell Biology ◽

10.1083/jcb.200804078 ◽

2008 ◽

Vol 183 (7) ◽

pp. 1193-1202 ◽

Cited By ~ 40

Author(s):

Owen J. Marshall ◽

Alan T. Marshall ◽

K.H. Andy Choo

Keyword(s):

Chromatin Immunoprecipitation ◽

Protein A ◽

Three Dimensional ◽

Higher Order ◽

Order Structure ◽

Mitotic Chromosomes ◽

Centromeric Chromatin ◽

Centromere Protein A ◽

Transmission Electron ◽

Histone H3 Variant

The histone H3 variant centromere protein A (CENP-A) is central to centromere formation throughout eukaryotes. A long-standing question in centromere biology has been the organization of CENP-A at the centromere and its implications for the structure of centromeric chromatin. In this study, we describe the three-dimensional localization of CENP-A at the inner kinetochore plate through serial-section transmission electron microscopy of human mitotic chromosomes. At the kinetochores of normal centromeres and at a neocentromere, CENP-A occupies a compact domain at the inner kinetochore plate, stretching across two thirds of the length of the constriction but encompassing only one third of the constriction width and height. Within this domain, evidence of substructure is apparent. Combined with previous chromatin immunoprecipitation results (Saffery, R., H. Sumer, S. Hassan, L.H. Wong, J.M. Craig, K. Todokoro, M. Anderson, A. Stafford, and K.H.A. Choo. 2003. Mol. Cell. 12:509–516; Chueh, A.C., L.H. Wong, N. Wong, and K.H.A. Choo. 2005. Hum. Mol. Genet. 14:85–93), our data suggest that centromeric chromatin is arranged in a coiled 30-nm fiber that is itself coiled or folded to form a higher order structure.

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Antisera to gamma-aminobutyric acid. III. Demonstration of GABA in Golgi-impregnated neurons and in conventional electron microscopic sections of cat striate cortex.

Journal of Histochemistry & Cytochemistry ◽

10.1177/33.3.2579124 ◽

1985 ◽

Vol 33 (3) ◽

pp. 249-257 ◽

Cited By ~ 308

Author(s):

P Somogyi ◽

A J Hodgson

Keyword(s):

Striate Cortex ◽

Protein A ◽

Three Dimensional ◽

Aminobutyric Acid ◽

Gamma Aminobutyric Acid ◽

Electron Microscopic ◽

Golgi Impregnation ◽

Second Procedure ◽

Unlabeled Antibody ◽

Layer Vi

Two methods are described for the immunocytochemical demonstration of immunoreactive gamma-aminobutyric acid (GABA) in the visual cortex of the cat, an area that contains several types of GABAergic neurons and requires combined methods for their characterization. The first method is illustrated by a representative example of a Golgi-impregnated and gold-toned interneuron of the "bitufted" type situated in layer VI and having an ascending axon. After recording the three-dimensional features of the cell, semithin (0.5 micron) sections of the perikaryon were cut and GABA was demonstrated in the cell body by the unlabeled antibody enzyme method. While immunocytochemistry was used to determine the probable transmitter of the neuron, Golgi-impregnation of the same cell was used to identify its neuronal type. Since aldehyde-osmium fixation was used, further electron microscopic (EM) analysis of the neuron's synaptic connections was possible. The second procedure demonstrated GABA in EM sections of aldehyde-osmium-fixed cortex using protein A-gold as an immunocytochemical marker. Immunoreactivity was found in certain neurons, dendrites, axons, and boutons forming type II synaptic contacts that from previous studies have been thought to be GABAergic. Thus ultrastructural analysis using optimal conditions can now be supplemented with the identification of the transmitter in the same section.

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Identification of biomolecules for Alzheimer's disease using docking analysis of tau protein

NeuroPharmac Journal ◽

10.37881/1.617 ◽

2021 ◽

pp. 192-203

Author(s):

Mansi Agrahari ◽

Kanu Megha ◽

Kajal Dahiya ◽

Ila Sharma ◽

Ankur Sharma ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Tau Protein ◽

Active Site ◽

Protein A ◽

Three Dimensional ◽

Docking Studies ◽

Dimensional Structure ◽

Docking Analysis ◽

Bioinformatic Tools

Objective: In-silico methods to find and characterize the ligands against the active site of tau protein which could assist in the therapeutics of Alzheimer's disease. Methods: The aid of various bioinformatic tools such as phylogenetic analysis, homology modeling, and active site prediction led to the molecular docking analysis of the major malefactor for Alzheimer’s disease ‘microtubule- associated tau protein’. A three-dimensional structure of microtubule-related tau protein was created, and the Ramachandran plot was acquired for quality appraisal. Results: Procheck showed 62.95 of residues in the most preferred region with 20% residues in the additional allowed region and 5.7 % in the disallowed region of microtubule-associated tau protein. Screenings of the particles were done dependent on Lipinski's standard of five. Conclusion: Genistein, Hesperidin, and epigallocatechin-3 are the potential ligands in regulating microtubule-related tau protein and Epigallocatechin-3 gallate is the most potent among them and the most elevated negative free vitality of official with the maximum interacting surface territory throughout docking studies.

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Crystallization of Membrane Proteins

Crystallization of Nucleic Acids and Proteins ◽

10.1093/oso/9780199636792.003.0013 ◽

1999 ◽

Author(s):

F. Reiss-Husson ◽

D. Picot

Keyword(s):

Membrane Proteins ◽

Membrane Protein ◽

Protein A ◽

Limited Proteolysis ◽

Three Dimensional ◽

Hydrophobic Surface ◽

Biological Macromolecules ◽

Recent Developments ◽

Tight Association ◽

Membrane Components

Crystallization of membrane proteins is one of the most recent developments in protein crystal growth; in 1980, for the first time, two membrane proteins were successfully crystallized, bacteriorhodopsin (1) and porin (2). Since then, a number of membrane proteins (about 30) yielded three-dimensional crystals. In several cases, the quality of the crystals was sufficient for X-ray diffraction studies. The first atomic structure of a membrane protein, a photosynthetic bacterial reaction centre, was described in 1985 (3), followed by the structure of about ten other membrane protein families. Crystallization of membrane proteins is now an actively growing field, and has been discussed in several recent reviews (4-8). The major difficulty in the study of membrane proteins, which for years hampered their crystallization, comes from their peculiar solubility properties. These originate from their tight association with other membrane components, particularly lipids. Indeed integral membrane proteins contain hydrophobic surface regions buried in the lipid bilayer core, as well as hydrophilic regions with charged or polar residues more or less exposed at the external faces of the membrane. Disruption of the bilayer for isolating a membrane protein can be done in various ways: extraction with organic solvents, use of chaotropic agents, or solubilization by a detergent. The last method is the most frequently used, since it maintains the biological activity of the protein if a suitable detergent is found. This chapter will be restricted to specific aspects of three-dimensional crystallizations done in micellar solutions of detergent. In some cases, it is possible to separate soluble domains from the membrane protein either by limited proteolysis or by genetic engineering. Such protein fragments can then be treated as soluble proteins and so will not be discussed further in this chapter. We refer to Chapter 12 and the review by Kühlbrandt (9) for the methodology of two-dimensional crystallization used for electron diffraction. The general principles discussed in this book for the crystallization of soluble biological macromolecules apply for membrane proteins; the protein solution must be brought to supersaturation by modifying its physical parameters (concentrations of constituents, ionic strength, and so on), so that nucleation may occur.

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A Nonfimbrial Adhesin ofAggregatibacter actinomycetemcomitansMediates Biofilm Biogenesis

Infection and Immunity ◽

10.1128/iai.00704-18 ◽

2018 ◽

Vol 87 (1) ◽

Cited By ~ 2

Author(s):

David R. Danforth ◽

Gaoyan Tang-Siegel ◽

Teresa Ruiz ◽

Keith P. Mintz

Keyword(s):

Biofilm Formation ◽

Protein A ◽

Three Dimensional ◽

Binding Activity ◽

Periodontal Pathogen ◽

Collagen Binding ◽

Content Type ◽

Mutant Strains ◽

Different Strains ◽

Biofilm Development

ABSTRACTPeriodontitis is an inflammatory disease caused by polymicrobial biofilms. The periodontal pathogenAggregatibacter actinomycetemcomitansdisplays two proteinaceous surface structures, the fimbriae and the nonfimbrial extracellular matrix binding protein A (EmaA), as observed by electron microscopy. Fimbriae participate in biofilm biogenesis and the EmaA adhesins mediate collagen binding. However, in the absence of fimbriae,A. actinomycetemcomitansstill retains the potential to form robust biofilms, suggesting that other surface macromolecules participate in biofilm development. Here, isogenic mutant strains lacking EmaA structures, but still expressing fimbriae, were observed to have reduced biofilm potential. In strains lacking both EmaA and fimbriae, biofilm mass was reduced by 80%. EmaA enhanced biofilm formation in different strains, independent of the fimbriation state or serotype. Confocal microscopy revealed differences in cell density within microcolonies between the EmaA positive and mutant strains. EmaA-mediated biofilm formation was found to be independent of the glycosylation state and the precise three-dimensional conformation of the protein, and thus this function is uncorrelated with collagen binding activity. The data suggest that EmaA is a multifunctional adhesin that utilizes different mechanisms to enhance bacterial binding to collagen and to enhance biofilm formation, both of which are important forA. actinomycetemcomitanscolonization and subsequent infection.

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