Exploring the Interplay of Sequence and Structural Features in Determiming the Flexibility of AGC Kinase Protein Family : A Bioinformatics Approach

2008 ◽  
Vol 01 (02) ◽  
pp. 077-089 ◽  
Author(s):  
Amit Kumar Banerjee ◽  
Neelima Arora ◽  
Varakantham Pranitha ◽  
U.S.N. Murty
Keyword(s):  
Structural Features ◽  
Protein Family

scholarly journals Structural Features and Chaperone Activity of the NudC Protein Family

2011 ◽  
Vol 409 (5) ◽  
pp. 722-741 ◽  
Author(s):  
Meiying Zheng ◽  
Tomasz Cierpicki ◽  
Alexander J. Burdette ◽  
Darkhan Utepbergenov ◽  
Paweł Ł. Janczyk ◽  
...  
Keyword(s):  
Structural Features ◽  
Protein Family ◽  
Chaperone Activity

scholarly journals Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p

2021 ◽  
Vol 478 (3) ◽  
pp. 579-595
Author(s):  
Melanie H. Dietrich ◽  
Li-Jin Chan ◽  
Amy Adair ◽  
Sravya Keremane ◽  
Phillip Pymm ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Life Cycle ◽  
Vaccine Development ◽  
Structural Information ◽  
Family Members ◽  
Structural Features ◽  
Protein Family ◽  
Parasite Life Cycle ◽  
D2 Domain

Surface-associated proteins play critical roles in the Plasmodium parasite life cycle and are major targets for vaccine development. The 6-cysteine (6-cys) protein family is expressed in a stage-specific manner throughout Plasmodium falciparum life cycle and characterized by the presence of 6-cys domains, which are β-sandwich domains with conserved sets of disulfide bonds. Although several 6-cys family members have been implicated to play a role in sexual stages, mosquito transmission, evasion of the host immune response and host cell invasion, the precise function of many family members is still unknown and structural information is only available for four 6-cys proteins. Here, we present to the best of our knowledge, the first crystal structure of the 6-cys protein Pf12p determined at 2.8 Å resolution. The monomeric molecule folds into two domains, D1 and D2, both of which adopt the canonical 6-cys domain fold. Although the structural fold is similar to that of Pf12, its paralog in P. falciparum, we show that Pf12p does not complex with Pf41, which is a known interaction partner of Pf12. We generated 10 distinct Pf12p-specific nanobodies which map into two separate epitope groups; one group which binds within the D2 domain, while several members of the second group bind at the interface of the D1 and D2 domain of Pf12p. Characterization of the structural features of the 6-cys family and their associated nanobodies provide a framework for generating new tools to study the diverse functions of the 6-cys protein family in the Plasmodium life cycle.

scholarly journals Novel ATPase of SNF2-like Protein Family Interacts with Androgen Receptor and Modulates Androgen-dependent Transcription

2002 ◽  
Vol 13 (6) ◽  
pp. 2106-2119 ◽  
Author(s):  
Nathalie Rouleau ◽  
Andrii Domans'kyi ◽  
Mati Reeben ◽  
Anu-Maarit Moilanen ◽  
Kristina Havas ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Atpase Activity ◽  
Mammalian Cells ◽  
Structural Features ◽  
Protein Family ◽  
Dominant Negative ◽  
Dependent Manner ◽  
Interacting Protein ◽  
Target Promoter

Nuclear receptors, including the androgen receptor (AR), regulate target cell transcription through interaction with auxiliary proteins to modify chromatin structure. We describe herein a novel AR-interacting protein, termed ARIP4, that has structural features typical of the SNF2-like protein family. With regard to the Snf2 domain, the closest homolog of ARIP4 is the ATRX protein. ARIP4 is a nuclear protein and comprises 1466 amino acids. It interacts with AR in vitro and in cultured yeast and mammalian cells. ARIP4 can be labeled with 8-azido-[γ-32P]ATP and exhibits DNA-dependent ATPase activity. Like several ATP-dependent chromatin remodeling proteins, ARIP4 generates superhelical torsion within linear DNA fragments in an ATP-dependent manner. With a stably integrated target promoter, ARIP4 elicits a modest enhancement of AR-dependent transactivation. In transient cotransfection assays, ARIP4 modulates AR function in a promoter-dependent manner; it enhances receptor activity on minimal promoters, but does not activate more complex promoters. ARIP4 mutants devoid of ATPase activity fail to alter DNA topology and behave as trans-dominant negative regulators of AR function in transient assays.

scholarly journals Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p

2020 ◽  
Author(s):  
Melanie H Dietrich ◽  
Li-Jin Chan ◽  
Amy Adair ◽  
Sravya Keremane ◽  
Phillip Pymm ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Life Cycle ◽  
Vaccine Development ◽  
Structural Information ◽  
Family Members ◽  
Structural Features ◽  
Protein Family ◽  
Parasite Life Cycle ◽  
D2 Domain

Surface-associated proteins play critical roles in the Plasmodium parasite life cycle and are major targets for vaccine development. The 6-cysteine (6-cys) protein family is expressed in a stage-specific manner throughout Plasmodium falciparum life cycle and characterized by the presence of 6-cys domains, which are β-sandwich domains with conserved sets of disulfide bonds. Although several 6-cys family members have been implicated to play a role in sexual stages, mosquito transmission, evasion of the host immune response and host cell invasion, the precise function of many family members is still unknown and structural information is only available for four 6-cys proteins. Here, we present to the best of our knowledge, the first crystal structure of the 6-cys protein Pf12p determined at 2.8 Å resolution. The monomeric molecule folds into two domains, D1 and D2, both of which adopt the canonical 6-cys domain fold. Although the structural fold is similar to that of Pf12, its paralog in P. falciparum, we show that Pf12p does not complex with Pf41, which is a known interaction partner of Pf12. We generated ten distinct Pf12p-specific nanobodies which map into two separate epitope groups; one group which binds within the D2 domain, while several members of the second group bind at the interface of the D1 and D2 domain of Pf12p. Characterization of the structural features of the 6-cys family and their associated nanobodies provide a framework for generating new tools to study the diverse functions of the 6-cys protein family in the Plasmodium life cycle.

Evolution of the Na-Picotransport systems

2001 ◽  
Vol 280 (2) ◽  
pp. R301-R312 ◽  
Author(s):  
Andreas Werner ◽  
Rolf K. H. Kinne
Keyword(s):  
Structural Features ◽  
Protein Family ◽  
Transport Systems ◽  
Vertebrate Development ◽  
Degenerate Primers ◽  
Homologous Proteins ◽  
C Elegans ◽  
Vertical Relationship ◽  
Membrane Transport Systems ◽  
Mammalian Protein

Membrane transport systems for Pitransport are key elements in maintaining homeostasis of Piin organisms as diverse as bacteria and human. Two Na-Picotransporter families with well-described functional properties in vertebrates, namely NaPi-II and NaPi-III, show conserved structural features with prokaryotic origin. A clear vertical relationship can be established among the mammalian protein family NaPi-III, a homologous system in C. elegans, the yeast system Pho89, and the bacterial Pitransporter Pit. An alternative lineage connects the mammalian NaPi-II-related transporters with homologous proteins from Caenorhabditis elegans and Vibrio cholerae. The present review focuses on the molecular evolution of the NaPi-II protein family. Preliminary results indicate that the NaPi-II homologue cloned from V. cholerae is indeed a functional Pitransporter when expressed in Xenopus oocytes. The closely related NaPi-II isoforms NaPi-IIa and NaPi-IIb are responsible for regulated epithelial Na-dependent Pitransport in all vertebrates. Most species express two different NaPi-II proteins with the exception of the flounder and Xenopus laevis, which rely on only a single isoform. Using an RT-PCR-based approach with degenerate primers, we were able to identify NaPi-II-related mRNAs in a variety of vertebrates from different families. We hypothesize that the original NaPi-IIb-related gene was duplicated early in vertebrate development. The appearance of NaPi-IIa correlates with the development of the mammalian nephron.

scholarly journals The pur protein family: Genetic and structural features in development and disease

2013 ◽  
Vol 228 (5) ◽  
pp. 930-937 ◽  
Author(s):  
Edward M. Johnson ◽  
Dianne C. Daniel ◽  
Jennifer Gordon
Keyword(s):  
Structural Features ◽  
Protein Family

scholarly journals Intracellular lipid binding protein family diversity from Oyster Crassostrea gigas: genomic and structural features of invertebrate lipid transporters

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Guilherme de Toledo-Silva ◽  
Guilherme Razzera ◽  
Flavia Lucena Zacchi ◽  
Nestor Cubas Wendt ◽  
Jacó Joaquim Mattos ◽  
...  
Keyword(s):  
Crassostrea Gigas ◽  
Binding Protein ◽  
Structural Features ◽  
Lipid Binding ◽  
Protein Family ◽  
Intracellular Lipid ◽  
Lipid Binding Protein ◽  
Family Diversity ◽  
Lipid Transporters
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