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Engineered Holliday Junctions as Single-Molecule Reporters for Protein−DNA Interactions with Application to a MerR-Family Regulator

Susanta K. Sarkar, Nesha May Andoy, Jaime J. Benítez, Peng R. Chen, Jason S. Kong, Chuan He, Peng Chen
2007 Journal of the American Chemical Society  
Both apo-and holo-PbrR691 bind the stacked conformers of the engineered HJ, change their structures, constrain their conformational distributions, alter the kinetics, and shift the equilibrium of their  ...  Here, we present a novel and generalizable method of using engineered DNA Holliday junctions (HJs) that contain specific protein-recognition sequences to report protein-DNA interactions in single-molecule  ...  experiments for PbrR691-HJ1 interaction specificity, and an application of engineered HJ to study CueR-DNA interactions.  ... 
doi:10.1021/ja072485y pmid:17880214 pmcid:PMC2528078 fatcat:qevl4aigojcdhpksim3rqeea4y

Petri Nets Simulation for Operational Analytics Based on Process Data: An Overview

Natanael Yabes Wirawan, Riska Asriana Sutrisnowati, Sunghyun Sim, Nur Ichsan Utama, Nur Ahmad Wahid, Taufik Nur Adi, Yulim Choi, Imam Mustafa Kamal, Iq Reviessay Pulshashi, Hyerim Bae
2018 Innovative Computing Information and Control Express Letters, Part B: Applications  
Also, we incorporate into the framework several algorithms that are designed to handle large-sized data.  ...  ., distribution parameters, and simulation logic). Afterwards, we build the model by integrating the simulation parameters and process execution logics.  ...  The system interface is a REST API, which binds to the model integration and simulation engine.  ... 
doi:10.24507/icicelb.09.10.1033 fatcat:rqsyvvsfrra37abjlixzv43j4e

Hydrogel formation by multivalent IDPs: A reincarnation of the microtrabecular lattice?

Peter Tompa
2013 Intrinsically Disordered Proteins  
The transition is enabled by multiple distributed interactions between repetitive/low complexity regions of proteins, which tend to by structurally disordered.  ...  via altering their charge distributions, and the hydrogel actually has more than one stable physical states, which may undergo regulated transitions. 21 In the case of RNA-binding proteins, hydrogel  ... 
doi:10.4161/idp.24068 pmid:28516006 pmcid:PMC5424804 fatcat:qyzm5n7niffotjps3nqu5xpb4i

Improving the Development and Validation of Viewpoint Specifications [chapter]

N. Fischbeck, J. Fischer, E. Holz, O. Kath, M. Löwis, R. Schröder
1997 IFIP Advances in Information and Communication Technology  
This paper presents an overview of the application of ITU -SOL for the development of distributed systems according to the RM-OOP.  ...  Furthermore, concepts and principles for a smooth, semi-automatic SOL based transition between viewpoints, which are currently under development, are sketched out.  ...  In order for two computational objects to interact, first their interfaces have to be bound by an implicit or explicit binding.  ... 
doi:10.1007/978-0-387-35261-9_14 fatcat:kjcz6e4y5zbd3lxr4ofhfpzhfe

Visualization of the Differential Transition State Stabilization within the Active Site Environment

Pawel Kedzierski, Pawel Wielgus, Adrian Sikora, W. Sokalski, Jerzy Leszczynski
2004 International Journal of Molecular Sciences  
This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues.  ...  A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented.  ...  PK thanks the Computational Center for Molecular Structure and Interactions (CCMSI) at Jackson State University, and the Foundation for Polish Science (FNP) for support.  ... 
doi:10.3390/i5040186 fatcat:sg7q6gvkxbf4hnynj4q74npjcm

High-Throughput Protein Structural Mapping using Transition Metal FRET

Xiaozhen Yu, Justin Taraska
2012 Biophysical Journal  
These results augment the existing models that describe concerted insertion and folding events, and highlight the ability of FRET to provide insight into the complex mechanisms of membrane protein folding  ...  Multiple donor sites were individually labeled with organic dyes while di-histidine metal binding acceptor sites were engineered into a-helices.  ...  As these residues are located close to the putative substrate binding groove and near residues stabilizing the transition state, they may undergo a restricted structural rearrangement arising from signal  ... 
doi:10.1016/j.bpj.2011.11.2199 fatcat:lrtxkpz4undlpp4foauw3zoqrm

Relation of Antiferromagnetic Structure to the Binding Energies of Some b.c.c. Transition Metals

Yee-Chuang Hsu
1951 Physical Review  
These three theories represent three different ap- proaches to the understanding of the binding of the transition metals.  ...  Welding engineers desire stable arcs; circuit breaker engineers want unstable arcs; designers of rectifiers strive to eliminate cathode arc spots from their anodes at all times.  ... 
doi:10.1103/physrev.83.975 fatcat:lknucqvzgnh2pgmbckvdgsqnge

A Comparison of Donor-Acceptor Distance Distributions Derived from Ensemble and Single-Pair FRET Measurements

Tanya A. Baldwin, Gi-Ho Kim, Tyrel R. Deutscher, Maria E. Moutsoglou, John M. Robinson
2012 Biophysical Journal  
These results augment the existing models that describe concerted insertion and folding events, and highlight the ability of FRET to provide insight into the complex mechanisms of membrane protein folding  ...  Multiple donor sites were individually labeled with organic dyes while di-histidine metal binding acceptor sites were engineered into a-helices.  ...  As these residues are located close to the putative substrate binding groove and near residues stabilizing the transition state, they may undergo a restricted structural rearrangement arising from signal  ... 
doi:10.1016/j.bpj.2011.11.2201 fatcat:ijd3s5cvwnag7bado3zfzmoza4

Thermodynamic principles for the engineering of pH-driven conformational switches and acid insensitive proteins

Peregrine Bell-Upp, Aaron C. Robinson, Steven T. Whitten, Erika L. Wheeler, Janine Lin, Wesley E. Stites, Bertrand García-Moreno E
2011 Biophysical Chemistry  
Acid unfolding is a structural transition driven by preferential H + binding to the acid unfolded state (U) over the native (N) state of a protein.  ...  What is less obvious is how they can be used to engineer pH switches in proteins.  ...  Acknowledgments This work was supported by NIH Grants ROI GM-073838 to B. G-M. E.  ... 
doi:10.1016/j.bpc.2011.06.016 pmid:21802194 pmcid:PMC3373021 fatcat:urdlg3kwlvc5pokt5e3w5qlwwe

Fluorescence enhancement of a ligand-activated fluorescent protein induced by collective noncovalent interactions

Euihyun Lee, Sang-Hee Shim, Minhaeng Cho
2018 Chemical Science  
The fluorescence of fluorescent proteins with noncovalently encapsulated chromophore is enhanced by complex interactions between chromophore, protein and bound water.  ...  are oen needed to engineer those infrared FPs.  ...  In fact, water molecules in the binding pocket in V2T do not show any specic binding patterns, but are distributed broadly, indicating very weak BR-water interactions (Fig. 5f, black line) .  ... 
doi:10.1039/c8sc03558j pmid:30542580 pmcid:PMC6249632 fatcat:ag2ug5dcwrf4npfvj4sfkw5o44

A functionally conserved basic residue in glutathione transferases interacts with the glycine moiety of glutathione and is pivotal for enzyme catalysis

Ardcharaporn Vararattanavech, Albert J. Ketterman
2007 Biochemical Journal  
In addition to contributing to glutathione binding, this region also had major effects on enzyme catalysis, as shown by changes in kinetic parameters and substrate-specific activity.  ...  The present study characterized conserved residues in a GST (glutathione transferase) in the active-site region that interacts with glutathione.  ...  transition states upon GSH binding.  ... 
doi:10.1042/bj20070422 pmid:17523921 pmcid:PMC1948969 fatcat:rln7xsibefhxnhewhmoib3al3m

Tackling metal regulation and transport at the single-molecule level

Peng Chen, Nesha May Andoy, Jaime J. Benítez, Aaron M. Keller, Debashis Panda, Feng Gao
2010 Natural product reports (Print)  
For example, how do metalloregulators and DNA interact dynamically to control gene expression to maintain healthy cellular metal level?  ...  Here we review recent advances in studying the dynamic interactions of macromolecular machineries for metal regulation and transport at the single-molecule level: (1) The development of engineered DNA  ...  Rosenzweig for their contributions to the research described in this article. We also thank the National Institute of Health (GM082939), National Science Foundation  ... 
doi:10.1039/b906691h pmid:20442963 pmcid:PMC2992825 fatcat:wulvhyqdgrbodi4noqeijsmh6y

Analysis of Size and Compositional Distributions of Pleomorphic Ensembles Arising from Clustering of Multivalent Biological Molecules

Cibele V. Falkenberg, Michael L. Blinov, Leslie M. Loew
2014 Biophysical Journal  
We seek to use molecular simulations to predict and understand protein-ligand interactions.  ...  Our approach uses so-called "alchemical" free energy calculations to quantitatively predict binding affinities.  ...  binding sites.  ... 
doi:10.1016/j.bpj.2013.11.1465 fatcat:lhrukcw3ynhsja543pfkqmpq4e

Single-Molecule Study of Metalloregulator CueR-DNA Interactions Using Engineered Holliday Junctions

Nesha May Andoy, Susanta K. Sarkar, Qi Wang, Debashis Panda, Jaime J. Benítez, Aleksandr Kalininskiy, Peng Chen
2009 Biophysical Journal  
Depending on their metal-binding states, the MerR-family metalloregulators change their interactions with DNA to suppress or activate transcription.  ...  To understand their functions fundamentally, we study how CueR, a Cu 1þ -responsive MerR-family metalloregulator, interacts with DNA, using an engineered DNA Holliday junction (HJ) as a protein-DNA interaction  ...  Apo-CueR initially binds to conf-II to form a complex (P-II) that can lead to structural transition to conf-I; this P-II complex can then bind a second protein molecule to form a tertiary complex (P 2  ... 
doi:10.1016/j.bpj.2009.05.027 pmid:19651042 pmcid:PMC2718160 fatcat:6tzw5hvtvbcstpx5udzjyfdfn4

Fluorescence Spectroscopy of Soluble E. Coli Spase I Demonstrates Conformational Changes Induced by Lipid and Signal Peptide Binding

Meera B. Kolayarattil, Sarah M. Auclair, Dongmei Yu, Debra A. Kendall
2012 Biophysical Journal  
These results augment the existing models that describe concerted insertion and folding events, and highlight the ability of FRET to provide insight into the complex mechanisms of membrane protein folding  ...  Multiple donor sites were individually labeled with organic dyes while di-histidine metal binding acceptor sites were engineered into a-helices.  ...  As these residues are located close to the putative substrate binding groove and near residues stabilizing the transition state, they may undergo a restricted structural rearrangement arising from signal  ... 
doi:10.1016/j.bpj.2011.11.2203 fatcat:4kxjiisofvbslo762ld2vqtpeq
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