scholarly journals Proteopedia.Org: A scientific “Wiki” bridging the rift between 3D structure and function of biomacromolecules

Biopolymers ◽  
2009 ◽  
Vol 92 (1) ◽  
pp. 76-77 ◽  
Author(s):  
Eric Martz
Keyword(s):  
3D Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Deciphering the 3D Structure and Function of Phosphofructokinase from Fission Yeast

2014 ◽  
Vol 20 (S3) ◽  
pp. 1246-1247
Author(s):  
Shaun Benjamin ◽  
Michael Radermacher ◽  
Teresa Ruiz
Keyword(s):  
Fission Yeast ◽  
3D Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Cohesin Releasing Factor WAPL Regulates Genome Structure and Function of Mature T Cells

2021 ◽  
Author(s):  
Yaping Sun ◽  
Gabrielle A. Dotson ◽  
Lindsey A. Muir ◽  
Scott Ronquist ◽  
Katherine Oravecz-Wilson ◽  
...  
Keyword(s):  
T Cells ◽  
Hematopoietic Cell Transplantation ◽  
Genome Structure ◽  
3D Structure ◽  
Three Dimensional ◽  
Structure And Function ◽  
Cell Functions ◽  
And Function

ABSTRACTThe cohesin complex modulates gene expression and cellular functions by shaping three-dimensional (3D) organization of chromatin. WAPL, cohesin’s DNA releasing factor, regulates 3D chromatin architecture. The 3D genome structure and its relevance to mature T cell functions is not well understood. We show that in vivo lymphopenic expansion, and allo-antigen driven proliferation, alters the 3D structure and function of the genome in mature T cells. Conditional deletion of Wapl in T cells reduced long-range genomic interactions, altered chromatin A/B compartments and the topologically associating domains (TAD) of the chromatin in T cells at baseline. Comparison of chromatin structure in normal and WAPL-deficient T cells after lymphopenic and allo-antigen driven stimulation revealed reduced loop extensions with changes in cell cycling genes. WAPL-mediated changes in 3D architecture of chromatin regulated activation, cycling and proliferation of T cells in vitro and in vivo. Finally, WAPL-deficient T cells caused reduced severity of graft-versus-host disease following experimental allogeneic hematopoietic cell transplantation. These data collectively characterize 3D genomic architecture of T cells in vivo and demonstrate biological and clinical implications for its disruption by cohesin releasing factor WAPL.

The 3D structure and function of digestive cathepsin L-like proteinases of Tenebrio molitor larval midgut

2012 ◽  
Vol 42 (9) ◽  
pp. 655-664 ◽  
Author(s):  
Daniela Beton ◽  
Cristiane R. Guzzo ◽  
Alberto F. Ribeiro ◽  
Chuck S. Farah ◽  
Walter R. Terra
Keyword(s):  
Cathepsin L ◽  
3D Structure ◽  
Tenebrio Molitor ◽  
Structure And Function ◽  
Larval Midgut ◽  
And Function

scholarly journals Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
N. Harathi ◽  
Madhusudana Pulaganti ◽  
C. M. Anuradha ◽  
Suresh Kumar Chitta
Keyword(s):  
Drug Targets ◽  
Rational Design ◽  
3D Structure ◽  
Reliability Assessment ◽  
Comparative Modeling ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
And Function ◽  
Key Residues

The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics. The reliability assessment of the built model was carried out with various protein checking tools such as Procheck, Whatif, ProsA, Errat, and Verify 3D. The obtained model investigates the relation between the structure and function. Molecular docking interactions of Mtb-RmlA with modified EMB (ethambutol) ligands and natural substrate have revealed specific key residues Arg13, Lys23, Asn109, and Thr223 which play an important role in ligand binding and selection. Compared to all EMB ligands, EMB-1 has shown better interaction with Mtb-RmlA model. The information thus discussed above will be useful for the rational design of safe and effective inhibitors specific to RmlA enzyme pertaining to the treatment of tuberculosis.

scholarly journals How membrane lipids control the 3D structure and function of receptors

2018 ◽  
Vol 5 (1) ◽  
pp. 22-35 ◽  
Author(s):  
Jacques Fantini ◽  
◽  
Francisco J. Barrantes ◽  
Keyword(s):  
Membrane Lipids ◽  
3D Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Identification and Computational Analysis of 3D-Structure Of MOCS1

2021 ◽  
Author(s):  
Maham Hamid ◽  
uzma habib ◽  
Javeria Batool ◽  
Arshemah Qaisar ◽  
Rehan Zafar Paracha
Keyword(s):  
Binding Sites ◽  
Biosynthetic Pathway ◽  
Computational Analysis ◽  
Tertiary Structure ◽  
3D Structure ◽  
Structure And Function ◽  
Molybdenum Cofactor ◽  
Recognition Method ◽  
And Function ◽  
Ramachandran Plots

Abstract Cyclic pyranopterin monophosphate (cPMP) is one of the most stable intermediates in Molybdenum cofactor (MoCo) biosynthetic pathway. In humans, synthesis of cPMP from Guanosine triphosphate (GTP) requires functional genes i.e. Molybdenum Cofactor Synthesis-1 (MOCS1) genes that contains for two catalytic proteins MOCS1A and MOCS1B. Importance of MOCS1A and MOCS1B for biosynthesis of MoCo reveals from the fact that its deficiency leads to MoCo type A deficiency. As there is no structure available for MOCS1 genes in the literature, tertiary structure of MOCS1 genes were investigated in this research via threading or folds recognition method by i-TASSER and validation was done using ERRAT, Verify3D and Ramachandran plots. Binding sites were predicted and validated. Docking of MOCS1A with GTP and MOCS1B with 3, 8 dihydroguanosine was done using Autodock via PyRx. Apart from this, highly confident mutations were also predicted using SIFT and polyphen2 that can alter the structure and function of MOCS1 gene.

Proteopedia ‐ a Scientific 'Wiki' Bridging the Rift Between 3D Structure and Function of Biomacromolecules

2009 ◽  
Vol 23 (S1) ◽  
Author(s):  
Joel L. Sussman ◽  
Eran Hodis ◽  
Jaime Prilusky ◽  
Eric Martz
Keyword(s):  
3D Structure ◽  
Structure And Function ◽  
And Function
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