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Intrinsically Disordered Proteins (IDPs): Experimental and Computational Approaches in Drug Discovery

Suresh Kumar
2018 Drug Designing & Intellectual Properties International Journal  
Recently IDPs are getting importance as desirable drug targets for major diseases. This review introduces IDP's in drug discovery by experimental and by computational approach.  ...  Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions.  ...  Small-Angle Scattering of X-rays (SAXS): It is one of powerful method for characterization of both ordered and disordered proteins in solution.  ... 
doi:10.32474/ddipij.2018.01.000123 fatcat:3yeofbuv2vdyzbpiqb3xelv6iu

Characterization and inhibitor discovery of one novel malonyl-CoA: Acyl carrier protein transacylase (MCAT) fromHelicobacter pylori

Weizhi Liu, Cong Han, Lihong Hu, Kaixian Chen, Xu Shen, Hualiang Jiang
2006 FEBS Letters  
Enzymatic characterization of HpMCAT showed that the K m value for malonyl-CoA was 21.01 ± 2.3 lM, and the thermal-and guanidinium hydrochloride-induced unfolding processes for HpMCAT were quantitatively  ...  This current work is hoped to supply useful information for better understanding the MCAT features of H. pylori strain, and corytuberine might be used as a potential lead compound in the discovery of the  ...  the ability of the denaturant to unfold a protein.  ... 
doi:10.1016/j.febslet.2005.12.085 pmid:16413022 fatcat:et63adugcnbhzhbex32ecn4zha

Thermodynamic studies for drug design and screening

Nichola C Garbett, Jonathan B Chaires
2012 Expert Opinion on Drug Discovery  
Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically-driven  ...  Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions.  ...  FTSA is a broadly applicable screening method independent of any knowledge of the type or function of a biomolecule.  ... 
doi:10.1517/17460441.2012.666235 pmid:22458502 pmcid:PMC3496183 fatcat:2jt2bglwhfdgpfjrdmvinu53eq

Dihydrofolate reductase and membrane translocation: evolution of a classic experiment

André Schneider
2018 EMBO Reports  
As a consequence "reading" a manuscript often means just skimming through the abstract, having a glimpse at the figures and in some cases searching the PDF file for keywords of immediate interest.  ...  However, fact is classic papers still have a lot to offer. For once they withstood the test of the time, which means we know the reported results are correct and reproducible.  ...  -Thus, we have shown that the Eilers and Schatz experiment in combination with cutting edge proteomic methods can be used to characterize a protein import system without prior knowledge of any of its subunits  ... 
doi:10.15252/embr.201745692 pmid:29459483 pmcid:PMC5836104 fatcat:iv63vzlbdjaqnoqyujgrlifbji

Folding and Mis-Folding of Peptides and Proteins: Insights from Molecular Simulations

Giacomo De Mori, Massimiliano Meli, Luca Monticelli, Giorgio Colombo
2005 Mini-Reviews in Medical Chemistry  
Starting from unfolding simulations, through biased simulations, which require a knowledge of the native state conformation, to folding studies based on the simple knowledge of the protein (or peptide)  ...  Finally, we will give a critical outlook on the possible development of this field in the near future.  ...  a knowledge of the native state, which is used either as a starting point for unfolding, or as the target for biased MD simulations.  ... 
doi:10.2174/1389557053544038 pmid:15853625 fatcat:gini5yx6o5cp3l6j2ya3dvocly

Protein Folding and Misfolding: A Perspective from Theory

Naeem A Khan TA
2015 Journal of Glycomics & Lipidomics  
selection has influenced the properties of a molecular system for functional advantage.  ...  The understanding of folding of proteins into their compact three-dimensional structures, example of complex biological self-assembly process, will provide an insight into the way in which evolutionary  ...  Acknowledgement The authors are highly thankful for the facilities obtained at AMU Aligarh. Conflicts of interest The authors declare that there is no conflict of interest.  ... 
doi:10.4172/2153-0637.1000128 fatcat:tvnorgoev5e2xcglujo2jfb5ke

Going Small: Using Biophysical Screening to Implement Fragment Based Drug Discovery [chapter]

John J. Bowling, William R. Shadrick, Elizabeth C. Griffith, Richard E. Lee
2016 Special Topics in Drug Discovery  
A general description of metrics that are being used in the progression of fragment hits, the need for orthogonal assay testing, and guidance on potential pitfalls are included to assist scientists, considering  ...  Screening against biochemical targets with compact chemical fragments has developed a reputation as a successful early-stage drug discovery approach, thanks to recent drug approvals.  ...  We thank Cherise Guess, PhD, ELS, of the SJCRH Department of Scientific Editing for her assistance with editing.  ... 
doi:10.5772/66423 fatcat:katjlgt7ardn3izqzsf7hbipsi

Force probing cell shape changes to molecular resolution

Martin P. Stewart, Yusuke Toyoda, Anthony A. Hyman, Daniel J. Muller
2011 TIBS -Trends in Biochemical Sciences. Regular ed  
However, using SMFS to characterize cellular processes inside the living cell remains a challenge for the future [11] .  ...  Upon further separation a mechanical stress is applied and the elastic molecule becomes elongated. If the molecule is a protein it can unfold.  ...  Forschung (BMBF), Japan Society for Promotion of Science (JSPS) and the ETH Zü rich is greatly acknowledged.  ... 
doi:10.1016/j.tibs.2011.05.001 pmid:21646023 fatcat:32paxhuwz5buxjw7pdzl7jmwza

Glycan Biosynthesis: Structure, Information, and Heterogeneity

Anjali Jaiman, Mukund Thattai
2015 Biophysical Journal  
I will review the approach of coarse-grained molecular simulations for the investigation of protein folding and protein-protein interactions in a cellular environment, particularly the one for the research  ...  to the discovery of novel antibiotics for bacterial infections and antibiotic resistance worldwide.  ... 
doi:10.1016/j.bpj.2014.11.2026 fatcat:qtrsbrls6baevizz5wrlhihywu

Clinical proteomics and OMICS clues useful in translational medicine research

Elena López, Luis Madero, Juan López-Pascual, Martin Latterich
2012 Proteome Science  
Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems  ...  This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus  ...  In the post-genome era, the field of proteomics has incited great interest in the pursuit of protein/peptide biomarker discovery especially since MS has been shown to be capable of characterizing a large  ... 
doi:10.1186/1477-5956-10-35 pmid:22642823 pmcid:PMC3536680 fatcat:qigbjg5yqfgd3bzsj53bocrewe

Clinical Proteomics and Omics Clues Useful in Translational Medicine Research [chapter]

Elena López, Luis Madero, Juan López-Pascual, Martin Latterich
2014 Omics in Clinical Practice  
Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems  ...  This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus  ...  In the post-genome era, the field of proteomics has incited great interest in the pursuit of protein/peptide biomarker discovery especially since MS has been shown to be capable of characterizing a large  ... 
doi:10.1201/b17137-8 fatcat:c5jfa6qjyvhk5ill7xyuwuqcme

Protein Folding and Recognition in the Cell -- an in Silico Approach

Margaret S. Cheung
2015 Biophysical Journal  
Analytic methods -including NMR, mass-spectrometry, and glycan arrays -now permit the routine profiling of glycans associated with various cells or proteins.  ...  The biggest challenge today is to assimilate the wealth of information generated in this process into a conceptual framework.  ...  I will review the approach of coarse-grained molecular simulations for the investigation of protein folding and protein-protein interactions in a cellular environment, particularly the one for the research  ... 
doi:10.1016/j.bpj.2014.11.2031 fatcat:5tpjgsa2h5ebppz7hfd7y6fa7y

Molecular Mechanism of Protein Folding in the Cell

James E. Rothman, Randy Schekman
2011 Cell  
will share this year's Lasker Basic Medical Science Award for the discovery of the cell's protein-folding machinery, exemplified by cage-like structures that convert newly synthesized proteins into their  ...  Their fundamental findings reveal mechanisms that operate in normal physiologic processes and help to explain the problems that arise in diseases of protein folding.  ...  a coherent picture of the physiologic and biophysical processes that cells use to fold proteins.  ... 
doi:10.1016/j.cell.2011.08.041 pmid:21907398 fatcat:35dnc4atond5vazjptn7yixieu

Bacterial Outer Membranes and Interactions with Membrane Proteins

Wonpil Im
2015 Biophysical Journal  
Analytic methods -including NMR, mass-spectrometry, and glycan arrays -now permit the routine profiling of glycans associated with various cells or proteins.  ...  The biggest challenge today is to assimilate the wealth of information generated in this process into a conceptual framework.  ...  I will review the approach of coarse-grained molecular simulations for the investigation of protein folding and protein-protein interactions in a cellular environment, particularly the one for the research  ... 
doi:10.1016/j.bpj.2014.11.2030 fatcat:56kewptugbbjhgsyfuizroepdi

Large-Scale Machine Learning Approaches for Molecular Biophysics

Arvind Ramanathan, Chakra S. Chennubhotla, Pratul K. Agarwal, Christopher B. Stanley
2015 Biophysical Journal  
Analytic methods -including NMR, mass-spectrometry, and glycan arrays -now permit the routine profiling of glycans associated with various cells or proteins.  ...  The biggest challenge today is to assimilate the wealth of information generated in this process into a conceptual framework.  ...  I will review the approach of coarse-grained molecular simulations for the investigation of protein folding and protein-protein interactions in a cellular environment, particularly the one for the research  ... 
doi:10.1016/j.bpj.2014.11.2027 fatcat:cm3heuxiebgrfiqkb5xitit3ma
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