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Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluís Gelpí, Modesto Orozco, David van der Spoel
2013 PLoS Computational Biology  
that are valid at the proteome level.  ...  After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded  ...  Anton Feenstra for critical reading of the manuscript and whose suggestions helped improve and clarify it. Author Contributions  ... 
doi:10.1371/journal.pcbi.1003393 pmid:24348236 pmcid:PMC3861036 fatcat:5p6fuh5fcfcshfo5seshfvkhsy

Biophysical Characterization of Therapeutic Proteins for Early Prediction of Manufacturability

Nesrine Chakroun, David Hilton, Paul A. Daldy
2014 Biophysical Journal  
Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ...  This study offers a novel perspective on the effect of chemical reactions on their catalysts and suggests future experiments to explore how the local heat released at each turnover affect an enzyme's internal  ... 
doi:10.1016/j.bpj.2013.11.3700 fatcat:crtgzihwvvfqth55cnb2ay2gda

The Heat Released by a Chemical Reaction Locally Enhanced the Enzyme Diffusion

Clement Riedel, Christian W.A. Wilson, Kambiz Hamadani, Kostas Tsekouras, Susan Marqusee, Steve Presse, Carlos Bustamante
2014 Biophysical Journal  
Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ...  This study offers a novel perspective on the effect of chemical reactions on their catalysts and suggests future experiments to explore how the local heat released at each turnover affect an enzyme's internal  ... 
doi:10.1016/j.bpj.2013.11.3701 fatcat:ceyklpezqnhufns3vlrkjniofq

Thermodynamic Stability of an Aging Proteome

Adam M.R. Graff, Michael Hazoglou, Ken A. Dill
2014 Biophysical Journal  
Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ...  This study offers a novel perspective on the effect of chemical reactions on their catalysts and suggests future experiments to explore how the local heat released at each turnover affect an enzyme's internal  ... 
doi:10.1016/j.bpj.2013.11.3697 fatcat:t3iidosmxfcxrg3akxx4ls2qv4

Lipid Disequilibrium Destabilized a Subset of Membrane Proteins

Guillaume Thibault
2014 Biophysical Journal  
Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ...  This study offers a novel perspective on the effect of chemical reactions on their catalysts and suggests future experiments to explore how the local heat released at each turnover affect an enzyme's internal  ... 
doi:10.1016/j.bpj.2013.11.3702 fatcat:7i5tgxxxpvdlnavxogfqf456qe

Investigation of Smart Responses of Human Serum Albumin in Fever Condition: An In Vitro Approach

Mostafa Rezaei-Tavirani, Reza Vafaei, Mona Zamanian-Azodi
2014 Biophysical Journal  
Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ...  This study offers a novel perspective on the effect of chemical reactions on their catalysts and suggests future experiments to explore how the local heat released at each turnover affect an enzyme's internal  ... 
doi:10.1016/j.bpj.2013.11.3698 fatcat:rxbrfzaznretbd4twby2qo67qa

Characterization of FGF-1 Mutant, K126D

Taylor Ghahremani
2014 Biophysical Journal  
Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ...  This study offers a novel perspective on the effect of chemical reactions on their catalysts and suggests future experiments to explore how the local heat released at each turnover affect an enzyme's internal  ... 
doi:10.1016/j.bpj.2013.11.3699 fatcat:vfvml4ldbvbapd7ut6vzmp7tda

A Proteomic-scale, Mass Spec-based Method to Probe Forced Unfolding within Cells

Dennis E. Discher, Christine Carag, Brian Chase
2009 Biophysical Journal  
The thermostability of the hybrid channel at pH 8 is similar to that of the wild type but is insensitive to pH changes.  ...  This supports the notion that the pH sensor of KcsA is located in the C-terminal domain.  ...  We explore the role of this frustration and the cooperativity of the prolines and the chromophore further by performing detailed simulations of GFP. 1690-Pos Board B534 A Proteomic-scale, Mass Spec-based  ... 
doi:10.1016/j.bpj.2008.12.1662 fatcat:opvr3vwvnvbkhov2rpi3sw2274

Exploring functional genomics for drug target and therapeutics discovery in Plasmodia

L. Birkholtz, A.C. van Brummelen, K. Clark, J. Niemand, E. Maréchal, M. Llinás, A.I. Louw
2008 Acta Tropica  
However, the application of functional genomics to post-genomics research of Plasmodia is still in comparatively early stages.  ...  This review presents the status quo of functional genomics of the malaria parasite including descriptions of the transcriptome, proteome and interactome.  ...  The goals of systems biology include the discovery of interacting networks and their controlling nodes by integration of complex and diverse biological datasets into one system, either at the cellular  ... 
doi:10.1016/j.actatropica.2007.10.013 pmid:18083131 fatcat:mdkrauofozbo3plyl3xnbtaodi

GCN4 Enhances the Stability of the Pore Domain of Potassium Channel KcsA

Zhiguang Yuchi, Victor P.T. Pau, Daniel S.C. Yang
2009 Biophysical Journal  
The thermostability of the hybrid channel at pH 8 is similar to that of the wild type but is insensitive to pH changes.  ...  This supports the notion that the pH sensor of KcsA is located in the C-terminal domain.  ...  We explore the role of this frustration and the cooperativity of the prolines and the chromophore further by performing detailed simulations of GFP. 1690-Pos Board B534 A Proteomic-scale, Mass Spec-based  ... 
doi:10.1016/j.bpj.2008.12.1660 fatcat:y2bhzlqbnfhz5cumupx2iqr3eu

Thermostabilization Due to Rigidity: A Case Study of Rubredoxin

Andrew J. Rader
2009 Biophysical Journal  
The thermostability of the hybrid channel at pH 8 is similar to that of the wild type but is insensitive to pH changes.  ...  This supports the notion that the pH sensor of KcsA is located in the C-terminal domain.  ...  We explore the role of this frustration and the cooperativity of the prolines and the chromophore further by performing detailed simulations of GFP. 1690-Pos Board B534 A Proteomic-scale, Mass Spec-based  ... 
doi:10.1016/j.bpj.2008.12.1664 fatcat:fkhn7vwd4bfilm67fbwq2admi4

Thermodynamic and Structural Origins for the Extreme Stability of Taq DNA Polymerase

Chin-Chi Liu, Yanling Yang, Vince LiCata
2009 Biophysical Journal  
The thermostability of the hybrid channel at pH 8 is similar to that of the wild type but is insensitive to pH changes.  ...  This supports the notion that the pH sensor of KcsA is located in the C-terminal domain.  ...  We explore the role of this frustration and the cooperativity of the prolines and the chromophore further by performing detailed simulations of GFP. 1690-Pos Board B534 A Proteomic-scale, Mass Spec-based  ... 
doi:10.1016/j.bpj.2008.12.1663 fatcat:zrncf4wgvfgqvnlouv5gwa2w64

Multilevel Modeling To Understand The Folding Hysteresis Of GFP

Shachi Gosavi, Benjamin Andrews, Patricia Jennings, Jose' Onuchic
2009 Biophysical Journal  
The thermostability of the hybrid channel at pH 8 is similar to that of the wild type but is insensitive to pH changes.  ...  This supports the notion that the pH sensor of KcsA is located in the C-terminal domain.  ...  We explore the role of this frustration and the cooperativity of the prolines and the chromophore further by performing detailed simulations of GFP. 1690-Pos Board B534 A Proteomic-scale, Mass Spec-based  ... 
doi:10.1016/j.bpj.2008.12.1661 fatcat:5s3p4axjwnfnpaobky6dtmucwu

Formation Of A Core In SDS Denatured States Of Rhodopsin

Arpana Dutta, Judith Klein-Seetharaman
2009 Biophysical Journal  
The thermostability of the hybrid channel at pH 8 is similar to that of the wild type but is insensitive to pH changes.  ...  This supports the notion that the pH sensor of KcsA is located in the C-terminal domain.  ...  We explore the role of this frustration and the cooperativity of the prolines and the chromophore further by performing detailed simulations of GFP. 1690-Pos Board B534 A Proteomic-scale, Mass Spec-based  ... 
doi:10.1016/j.bpj.2008.12.1665 fatcat:kjgmww3ebncgxjmkwy4froqtku

Effects of Tryptophan Mutation on the Thermal Stability and Catalytic Activity of Cold-Adapted Esterase At Ambient Temperatures

Sei-Heon Jang, Jerusha Boyineni, Junyoung Kim, ChangWoo Lee
2014 Biophysical Journal  
The influenza A M2 protein is a homotetrameric membrane protein that is vital to the viral life cycle.  ...  Previous work from our group used site-directed spin labeling electron paramagnetic resonance spectroscopy (SDSL-EPR) to probe the conformation and dynamics of M2 constructs consisting of the transmembrane  ...  Assessing, at a very early stage in the development process, the ease of manufacture (the manufacturability) would allow the candidates proteins to be ranked and thus help controlling the costeffectiveness  ... 
doi:10.1016/j.bpj.2013.11.3696 fatcat:ig7bzig7qveslidfrb6edqsmfe
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