scholarly journals Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae

2021 ◽  
Vol 8 ◽  
Author(s):  
Sundeep Chaitanya Vedithi ◽  
Sony Malhotra ◽  
Marta Acebrón-García-de-Eulate ◽  
Modestas Matusevicius ◽  
Pedro Henrique Monteiro Torres ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Schwann Cells ◽  
Protein Structures ◽  
Mycobacterium Leprae ◽  
Data Bank ◽  
Nerve Damage ◽  
Structural Proteomics ◽  
Bacterial Survival ◽  
Functional Sites

Leprosy, caused by Mycobacterium leprae (M. leprae), is treated with a multidrug regimen comprising Dapsone, Rifampicin, and Clofazimine. These drugs exhibit bacteriostatic, bactericidal and anti-inflammatory properties, respectively, and control the dissemination of infection in the host. However, the current treatment is not cost-effective, does not favor patient compliance due to its long duration (12 months) and does not protect against the incumbent nerve damage, which is a severe leprosy complication. The chronic infectious peripheral neuropathy associated with the disease is primarily due to the bacterial components infiltrating the Schwann cells that protect neuronal axons, thereby inducing a demyelinating phenotype. There is a need to discover novel/repurposed drugs that can act as short duration and effective alternatives to the existing treatment regimens, preventing nerve damage and consequent disability associated with the disease. Mycobacterium leprae is an obligate pathogen resulting in experimental intractability to cultivate the bacillus in vitro and limiting drug discovery efforts to repositioning screens in mouse footpad models. The dearth of knowledge related to structural proteomics of M. leprae, coupled with emerging antimicrobial resistance to all the three drugs in the multidrug therapy, poses a need for concerted novel drug discovery efforts. A comprehensive understanding of the proteomic landscape of M. leprae is indispensable to unravel druggable targets that are essential for bacterial survival and predilection of human neuronal Schwann cells. Of the 1,614 protein-coding genes in the genome of M. leprae, only 17 protein structures are available in the Protein Data Bank. In this review, we discussed efforts made to model the proteome of M. leprae using a suite of software for protein modeling that has been developed in the Blundell laboratory. Precise template selection by employing sequence-structure homology recognition software, multi-template modeling of the monomeric models and accurate quality assessment are the hallmarks of the modeling process. Tools that map interfaces and enable building of homo-oligomers are discussed in the context of interface stability. Other software is described to determine the druggable proteome by using information related to the chokepoint analysis of the metabolic pathways, gene essentiality, homology to human proteins, functional sites, druggable pockets and fragment hotspot maps.

scholarly journals Interleukin-4 Regulates the Expression of CD209 and Subsequent Uptake of Mycobacterium leprae by Schwann Cells in Human Leprosy

2010 ◽  
Vol 78 (11) ◽  
pp. 4634-4643 ◽  
Author(s):  
Rosane M. B. Teles ◽  
Stephan R. Krutzik ◽  
Maria T. Ochoa ◽  
Rosane B. Oliveira ◽  
Euzenir N. Sarno ◽  
...  
Keyword(s):  
Schwann Cell ◽  
Peripheral Nerve ◽  
Schwann Cells ◽  
Primary Cultures ◽  
Mycobacterium Leprae ◽  
Microbial Pathogens ◽  
Interleukin 4 ◽  
Common Mechanism ◽  
Specific Cell

ABSTRACT The ability of microbial pathogens to target specific cell types is a key aspect of the pathogenesis of infectious disease. Mycobacterium leprae, by infecting Schwann cells, contributes to nerve injury in patients with leprosy. Here, we investigated mechanisms of host-pathogen interaction in the peripheral nerve lesions of leprosy. We found that the expression of the C-type lectin, CD209, known to be expressed on tissue macrophages and to mediate the uptake of M. leprae, was present on Schwann cells, colocalizing with the Schwann cell marker, CNPase (2′,3′-cyclic nucleotide 3′-phosphodiesterase), along with the M. leprae antigen PGL-1 in the peripheral nerve biopsy specimens. In vitro, human CD209-positive Schwann cells, both from primary cultures and a long-term line, have a higher binding of M. leprae compared to CD209-negative Schwann cells. Interleukin-4, known to be expressed in skin lesions from multibacillary patients, increased CD209 expression on human Schwann cells and subsequent Schwann cell binding to M. leprae, whereas Th1 cytokines did not induce CD209 expression on these cells. Therefore, the regulated expression of CD209 represents a common mechanism by which Schwann cells and macrophages bind and take up M. leprae, contributing to the pathogenesis of leprosy.

RECOGNIZING COMPLEX, ASYMMETRIC FUNCTIONAL SITES IN PROTEIN STRUCTURES USING A BAYESIAN SCORING FUNCTION

2003 ◽  
Vol 01 (01) ◽  
pp. 119-138 ◽  
Author(s):  
LIPING WEI ◽  
RUSS B. ALTMAN
Keyword(s):  
Binding Sites ◽  
Calcium Binding ◽  
Active Sites ◽  
Large Scale ◽  
Protein Structures ◽  
Scoring Function ◽  
Chemical Properties ◽  
Data Bank ◽  
Functional Sites ◽  
Calcium Binding Sites

The increase in known three-dimensional protein structures enables us to build statistical profiles of important functional sites in protein molecules. These profiles can then be used to recognize sites in large-scale automated annotations of new protein structures. We report an improved FEATURE system which recognizes functional sites in protein structures. FEATURE defines multi-level physico-chemical properties and recognizes sites based on the spatial distribution of these properties in the sites' microenvironments. It uses a Bayesian scoring function to compare a query region with the statistical profile built from known examples of sites and control nonsites. We have previously shown that FEATURE can accurately recognize calcium-binding sites and have reported interesting results scanning for calcium-binding sites in the entire Protein Data Bank. Here we report the ability of the improved FEATURE to characterize and recognize geometrically complex and asymmetric sites such as ATP-binding sites and disulfide bond-forming sites. FEATURE does not rely on conserved residues or conserved residue geometry of the sites. We also demonstrate that, in the absence of a statistical profile of the sites, FEATURE can use an artificially constructed profile based on a priori knowledge to recognize the sites in new structures, using redoxin active sites as an example.

scholarly journals Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization

2004 ◽  
Vol 1 (1) ◽  
pp. 80-89
Author(s):  
Guido Dieterich ◽  
Dirk W. Heinz ◽  
Joachim Reichelt
Keyword(s):  
Genetic Disorders ◽  
Protein Structures ◽  
3D Structure ◽  
Data Bank ◽  
Mendelian Inheritance ◽  
Biological Information ◽  
Structure Comparison ◽  
3D Structures ◽  
Functional Sites ◽  
And Function

Abstract The 3D structures of biomacromolecules stored in the Protein Data Bank [1] were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT [2] entries as well InterPro [3] domains and function sites with the corresponding 3D-structures. OMIM [4] (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure comparison of protein structures stored in DALI [5] was condensed into single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be identified upon visualization.

scholarly journals The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure

2012 ◽  
Vol 287 (42) ◽  
pp. 34979-34991 ◽  
Author(s):  
Christopher C. Valley ◽  
Alessandro Cembran ◽  
Jason D. Perlmutter ◽  
Andrew K. Lewis ◽  
Nicholas P. Labello ◽  
...  
Keyword(s):  
Rational Design ◽  
Protein Structures ◽  
Data Bank ◽  
Unique Role ◽  
Hydrophobic Residues ◽  
Receptor Complexes ◽  
Affinity Ligand ◽  
Additional Stabilization ◽  
High Affinity Ligand

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1–1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins.

USING RIGIDITY ANALYSIS TO PROBE MUTATION-INDUCED STRUCTURAL CHANGES IN PROTEINS

2012 ◽  
Vol 10 (03) ◽  
pp. 1242010 ◽  
Author(s):  
FILIP JAGODZINSKI ◽  
JEANNE HARDY ◽  
ILEANA STREINU
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Structural Changes ◽  
Protein Structures ◽  
Data Bank ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Single Amino Acid ◽  
Fast Evaluation

Predicting the effect of a single amino acid substitution on the stability of a protein structure is a fundamental task in macromolecular modeling. It has relevance to drug design and understanding of disease-causing protein variants. We present KINARI-Mutagen, a web server for performing in silico mutation experiments on protein structures from the Protein Data Bank. Our rigidity-theoretical approach permits fast evaluation of the effects of mutations that may not be easy to perform in vitro, because it is not always possible to express a protein with a specific amino acid substitution. We use KINARI-Mutagen to identify critical residues, and we show that our predictions correlate with destabilizing mutations to glycine. In two in-depth case studies we show that the mutated residues identified by KINARI-Mutagen as critical correlate with experimental data, and would not have been identified by other methods such as Solvent Accessible Surface Area measurements or residue ranking by contributions to stabilizing interactions. We also generate 48 mutants for 14 proteins, and compare our rigidity-based results against experimental mutation stability data. KINARI-Mutagen is available at http://kinari.cs.umass.edu .

Higher-throughput approaches to crystallization and crystal structure determination

2008 ◽  
Vol 36 (4) ◽  
pp. 771-775 ◽  
Author(s):  
Mark J. Fogg ◽  
Anthony J. Wilkinson
Keyword(s):  
Crystal Structure ◽  
Structural Biology ◽  
Protein Structures ◽  
Data Bank ◽  
Structural Proteomics ◽  
Structural Determination ◽  
Ligation Independent Cloning ◽  
Structure Solution ◽  
Biology Laboratory ◽  
Automated Methods

In recent times, there has been a large increase in the number of protein structures deposited in the Protein Data Bank. Structural genomics initiatives have contributed to this expansion through their focus on high-throughput structural determination. This has fuelled advances in many of the techniques in the pipeline from gene to protein to crystal to structure. These include ligation-independent cloning methods, parallel purification systems, robotic crystallization devices and automated methods of crystal identification, data collection and, in some cases, structure solution. Some of these advances are described and discussed briefly with an emphasis on activities in the York Structural Biology Laboratory through its participation in the Structural Proteomics in Europe consortium.

scholarly journals Adherence of Mycobacterium leprae to Schwann cells in vitro

1986 ◽  
Vol 22 (3) ◽  
pp. 277-282 ◽  
Author(s):  
B. M. ITTY ◽  
R. MUKHERJEE ◽  
N. H. ANTIA
Keyword(s):  
Schwann Cells ◽  
Mycobacterium Leprae

scholarly journals Mycobacterium leprae-Specific, HLA Class II-Restricted Killing of Human Schwann Cells by CD4+Th1 Cells: A Novel Immunopathogenic Mechanism of Nerve Damage in Leprosy

2001 ◽  
Vol 166 (10) ◽  
pp. 5883-5888 ◽  
Author(s):  
Eric Spierings ◽  
Tjitske de Boer ◽  
Brigitte Wieles ◽  
Linda B. Adams ◽  
Enrico Marani ◽  
...  
Keyword(s):  
Schwann Cells ◽  
Mycobacterium Leprae ◽  
Class Ii ◽  
Nerve Damage ◽  
Hla Class Ii ◽  
Th1 Cells

Novel mechanisms in the immunopathogenesis of leprosy nerve damage: The role of Schwann cells, T cells and Mycobacterium leprae

2000 ◽  
Vol 78 (4) ◽  
pp. 349-355 ◽  
Author(s):  
Eric Spierings ◽  
Tjitske De Boer ◽  
Laurence Zulianello ◽  
Tom HM Ottenhoff
Keyword(s):  
T Cells ◽  
Schwann Cells ◽  
Mycobacterium Leprae ◽  
Nerve Damage

scholarly journals Current strategies for protein production and purification enabling membrane protein structural biology

2016 ◽  
Vol 94 (6) ◽  
pp. 507-527 ◽  
Author(s):  
Aditya Pandey ◽  
Kyungsoo Shin ◽  
Robin E. Patterson ◽  
Xiang-Qin Liu ◽  
Jan K. Rainey
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Structural Biology ◽  
Protein Production ◽  
Protein Structures ◽  
Data Bank ◽  
In Vitro Translation ◽  
Preparation Methods ◽  
Natural Hosts

Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10–15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

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