Molecular-level understanding of the hTAS2R1 receptor-bitter tasting tetra-peptide binding: a structural biology study based on computational approaches

2021 ◽  
Author(s):  
Fangfang Wang ◽  
Wei Yang ◽  
Bo Zhou
Keyword(s):  
Structural Biology ◽  
Molecular Level ◽  
Peptide Binding ◽  
Computational Approaches

Effective computational approaches for bitter-tasting peptides have been developed and analyzed in the present work.

scholarly journals Computational approaches to selecting and optimising targets for structural biology

Methods ◽  
2011 ◽  
Vol 55 (1) ◽  
pp. 3-11 ◽  
Author(s):  
Ian M. Overton ◽  
Geoffrey J. Barton
Keyword(s):  
Structural Biology ◽  
Computational Approaches

scholarly journals Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)–Ligand Binding: A Structural Biology Study Based on Computational Methods

ACS Omega ◽  
2020 ◽  
Vol 5 (33) ◽  
pp. 21145-21161
Author(s):  
Santhosh Kumar Nagarajan ◽  
Sathya Babu ◽  
Honglae Sohn ◽  
Thirumurthy Madhavan
Keyword(s):  
Ligand Binding ◽  
Structural Biology ◽  
Computational Methods ◽  
Molecular Level ◽  
Somatostatin Receptor

scholarly journals Comparative Pathogenesis and Systems Biology for Biodefense Virus Vaccine Development

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Gavin C. Bowick ◽  
Alan D. T. Barrett
Keyword(s):  
Systems Biology ◽  
Immune Responses ◽  
Vaccine Development ◽  
Molecular Level ◽  
Preclinical Development ◽  
Computational Approaches ◽  
Machine Learning Methods ◽  
Basic Understanding ◽  
Viral Attenuation ◽  
Virus Strains

Developing vaccines to biothreat agents presents a number of challenges for discovery, preclinical development, and licensure. The need for high containment to work with live agents limits the amount and types of research that can be done using complete pathogens, and small markets reduce potential returns for industry. However, a number of tools, from comparative pathogenesis of viral strains at the molecular level to novel computational approaches, are being used to understand the basis of viral attenuation and characterize protective immune responses. As the amount of basic molecular knowledge grows, we will be able to take advantage of these tools not only to rationally attenuate virus strains for candidate vaccines, but also to assess immunogenicity and safety in silico. This review discusses how a basic understanding of pathogenesis, allied with systems biology and machine learning methods, can impact biodefense vaccinology.

scholarly journals The Relevance of Structural Biology in Studying Molecules Involved in Parasite–Host Interactions: Potential for Designing New Interventions

2014 ◽  
Vol 67 (12) ◽  
pp. 1732 ◽  
Author(s):  
Lyndel Mason ◽  
Parisa Amani ◽  
Megan Cross ◽  
Joshua Baker ◽  
Ulla-Maja Bailey ◽  
...  
Keyword(s):  
Structural Biology ◽  
Molecular Level ◽  
Three Dimensional ◽  
Structural Features ◽  
Detailed Knowledge ◽  
Common Theme ◽  
Host Interactions ◽  
Genome Annotations ◽  
Structure Of Proteins ◽  
Biology Research

New interventions against infectious diseases require a detailed knowledge and understanding of pathogen–host interactions and pathogeneses at the molecular level. The combination of the considerable advances in systems biology research with methods to explore the structural biology of molecules is poised to provide new insights into these areas. Importantly, exploring three-dimensional structures of proteins is central to understanding disease processes, and establishing structure–function relationships assists in identification and assessment of new drug and vaccine targets. Frequently, the molecular arsenal deployed by invading pathogens, and in particular parasites, reveals a common theme whereby families of proteins with conserved three-dimensional folds play crucial roles in infectious processes, but individual members of such families show high levels of specialisation, which is often achieved through grafting particular structural features onto the shared overall fold. Accordingly, the applicability of predictive methodologies based on the primary structure of proteins or genome annotations is limited, particularly when thorough knowledge of molecular-level mechanisms is required. Such instances exemplify the need for experimental three-dimensional structures provided by protein crystallography, which remain an essential component of this area of research. In the present article, we review two examples of key protein families recently investigated in our laboratories, which could represent intervention targets in the metabolome or secretome of parasites.

scholarly journals Structural Biology and Structure–Function Relationships of Membrane Proteins

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 245
Author(s):  
Isabel Moraes ◽  
Andrew Quigley
Keyword(s):  
Membrane Proteins ◽  
Structure Function ◽  
Structural Biology ◽  
Molecular Level ◽  
Biological Complexity

To understand the biological complexity of life, one needs to investigate how biomolecules behave and interact with each other at a molecular level [...]

scholarly journals The World of Cyclic Dinucleotides in Bacterial Behavior

2020 ◽  
Author(s):  
Aline Dias da Purificação ◽  
Nathalia Marins de Azevedo ◽  
Gabriel Guarany de Araujo ◽  
Robson Francisco de Souza ◽  
Cristiane Rodrigues Guzzo
Keyword(s):  
Structural Biology ◽  
Environmental Conditions ◽  
Molecular Level ◽  
Genomic Data ◽  
Second Messenger ◽  
Structural Data ◽  
The World ◽  
Second Messenger Systems ◽  
Cyclic Dinucleotides ◽  
Novel Protein

The regulation of multiple bacterial phenotypes was found to depend on different cyclic di-nucleotides (CDNs) that constitute intracellular signalling second messenger systems. Most notably, c-di-GMP, along with proteins related to its synthesis, sensing and degradation, was identified as playing a central role in the switching from biofilm to planktonic modes of growth. Recently, this world has been under expansion, with the discoveries of other signalling CNDs in bacteria (c-di-AMP and cGAMP) and also in eukaryotes, novel protein and RNA receptors of CDNs, and the numerous functions related to these molecules. In this work, we comprehensively review and analyse the structural biology data about the systems that bacteria use to synthesise and recognise CDNs, detailing their interactions at molecular level with their products/ligands. Additional interesting observations were made, including that different receptor types can bind CDNs in similar conformations and that, based on genomic data, different CDN second messenger systems may coexist in many organisms. The large amount of sequence and structural data available allows a broad view of the importance of CDNs in bacteria, but how cells coordinate these molecules to ensure adaptation to changing environmental conditions is still open for much further exploration.

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