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Modelling sequential protein folding under kinetic control

F. P.E. Huard, C. M. Deane, G. R. Wood
2006 Bioinformatics  
We demonstrate the effect using simple HP lattice models and show that the cotranslational folding of proteins under kinetic control has a significant impact on the final conformation.  ...  Motivation: This study presents a novel investigation of the effect of kinetic control on cotranslational protein folding.  ...  Evidence of real protein models to be in kinetic traps is expected (if simulated sequentially under kinetic control) Folding is under kinetic control Mouse prion protein native conformation is  ... 
doi:10.1093/bioinformatics/btl248 pmid:16873473 fatcat:23vi6rb2uffyndagqeb6vaz4je

Kinetically Controlled Ligation for the Convergent Chemical Synthesis of Proteins

Duhee Bang, Brad L. Pentelute, Stephen B. H. Kent
2006 Angewandte Chemie International Edition  
Fully convergent synthesis of the model protein crambin from six peptide segments.  ...  We believe that kinetically controlled ligation will form the basis for a truly practical convergent chemical synthesis of proteins.  ... 
doi:10.1002/anie.200600702 pmid:16639756 fatcat:cvyh5qkfxzfozdmv2rvmbbpmom

Kinetically Controlled Ligation for the Convergent Chemical Synthesis of Proteins

Duhee Bang, Brad L. Pentelute, Stephen B. H. Kent
2006 Angewandte Chemie  
Fully convergent synthesis of the model protein crambin from six peptide segments.  ...  We believe that kinetically controlled ligation will form the basis for a truly practical convergent chemical synthesis of proteins.  ... 
doi:10.1002/ange.200600702 fatcat:wvaxkoplgvfalh2n2f5fu4igvu

Protein folding: The stepwise assembly of foldon units

H. Maity, M. Maity, M. M. G. Krishna, L. Mayne, S. W. Englander
2005 Proceedings of the National Academy of Sciences of the United States of America  
The folding pathway is determined by a sequential stabilization process; previously formed foldons guide and stabilize subsequent foldons to progressively build the native protein.  ...  Equilibrium and kinetic hydrogen exchange experiments show that cytochrome c is composed of five foldon units that continually unfold and refold even under native conditions.  ...  In summary, these stability labeling results favor a sequential unfolding model and therefore an equal and opposite refolding sequence, as in Eq. 2. Kinetic Folding Intermediate by HX Pulse Labeling.  ... 
doi:10.1073/pnas.0501043102 pmid:15774579 pmcid:PMC555724 fatcat:42cuzyobqbfknb7liotkiqfmjq

An Early Intermediate in the Folding Reaction of the B1 Domain of Protein G Contains a Native-like Core†

Soon-Ho Park, Karyn T. O'Neil, Heinrich Roder
1997 Biochemistry  
The folding kinetics of a 57-residue IgG binding domain of streptococcal protein G has been studied under varying solvent conditions, using stopped-flow fluorescence methods.  ...  Although GB1 has been cited as an example of a protein that obeys a two-state folding mechanism, the following kinetic observations suggest the presence of an early folding intermediate.  ...  Sauder for helpful advice on kinetic modeling and S. Seeholzer for mass spectrometry.  ... 
doi:10.1021/bi971914+ pmid:9400366 fatcat:vgknjxq42bfgbolz6dcxyk6z2m

The Effect of Disease-associated Mutations on the Folding Pathway of Human Prion Protein

Adrian C. Apetri, Krystyna Surewicz, Witold K. Surewicz
2004 Journal of Biological Chemistry  
Chem. 277, 44589 -44592) that the folding of wild-type prion protein can best be described by a three-state sequential model involving a partially folded intermediate.  ...  Here we have performed kinetic stopped-flow studies for a number of recombinant prion protein variants carrying mutations associated with familial forms of prion disease.  ...  Solid lines represent the best fit of the kinetic data to a three-state sequential folding model. FIG. 6.  ... 
doi:10.1074/jbc.m313581200 pmid:14761942 fatcat:245ccama7nc7pouhgmkjq5orhe

Protein folding and misfolding: mechanism and principles

S. Walter Englander, Leland Mayne, Mallela M. G. Krishna
2007 Quarterly Reviews of Biophysics (print)  
Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.  ...  It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships.  ...  Other datasets under other conditions with additional kinetic phases were equally well fit by both models but usually with fewer fitting constants for the PPOE model.  ... 
doi:10.1017/s0033583508004654 pmid:18405419 pmcid:PMC3433742 fatcat:kw2lrimeazaerj3ggzndo35v2i

Rapid Folding and Unfolding of Apaf-1 CARD

Sara L. Milam, Nathan I. Nicely, Brett Feeney, Carla Mattos, A. Clay Clark
2007 Journal of Molecular Biology  
Single mixing and sequential mixing stopped-flow studies showed that Apaf-1 CARD folds and unfolds rapidly and suggests a folding mechanism that contains parallel channels with two unfolded conformations  ...  This is in contrast to other CARDs in which folding appears to be dominated by formation of kinetic traps.  ...  Kinetic simulations The sequential mixing kinetic studies described above ruled out the sequential folding model shown in Scheme 1 because the native ensemble formed rapidly upon refolding, either in low  ... 
doi:10.1016/j.jmb.2007.02.105 pmid:17408690 pmcid:PMC2020445 fatcat:rki7c7g5wfafbpwy47yxp2hipi

Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR

Heinrich Roder, Gülnur A. Elöve, S. Walter Englander
1988 Nature  
To understand the process of protein folding, it will be necessary to obtain detailed structural information on folding intermediates.  ...  In particular, the rapid protection in the first kinetic phase exclusively for N-and C-terminal amide sites is characteristic of sequential folding behaviour.  ...  The small number of distinct kinetic phases suggests that refolding follows a limited number of pathways with discrete intermediates and argues against folding models with numerous parallel folding pathways  ... 
doi:10.1038/335700a0 pmid:2845279 pmcid:PMC3430852 fatcat:w5bbuzeer5gmxobc35tvhplkmi

Direct Observation of Parallel Folding Pathways Revealed Using a Symmetric Repeat Protein System

Tural Aksel, Doug Barrick
2014 Biophysical Journal  
The increase in folding rate with chain length, as opposed to a decrease expected from typical models for globular proteins, is a clear demonstration of parallel pathways.  ...  This finding of parallel pathways differs from results from kinetic studies of repeat-proteins composed of sequence-variable repeats, where modest repeat-to-repeat energy variation coalesces folding into  ...  The complexity in unfolding displayed by the model reflects the fact that, like the more complicated 82 parameter model, the kinetic Ising model includes multistate sequential folding (along each parallel  ... 
doi:10.1016/j.bpj.2014.04.058 pmid:24988356 pmcid:PMC4119276 fatcat:w6kb7vre3nauvm2htkihofywe4

Early aggregated States in the folding of interleukin-1β

J M Finke, P A Jennings
2001 Journal of biological physics (Print)  
This study indicates that (1) measured interleukin-1β folding kinetics fit to a 2 phase model and (2) at higher protein concentrations, transient association of IL-1β may result in a kinetic fit of 3 phases  ...  Experimental controls provide evidence that ANS binds to protein aggregates, present at higher concentrations and absent at lower concentrations.  ...  As a result, IL-1β provides a versatile system in which to study protein folding under conditions with and without aggregation.  ... 
doi:10.1023/a:1013178505077 pmid:23345738 pmcid:PMC3456583 fatcat:2rbw4p5dqnhebgqfkzru6emfay

Strange kinetic phase in the extremely early folding process of β-lactoglobulin

Yuji O. Kamatari, Hironori K. Nakamura, Kazuo Kuwata
2007 FEBS Letters  
A continuous-wave probed laser-induced temperature jump system was constructed and applied to monitor the changes in tryptophan fluorescence of the b-lactoglobulin during its folding; the kinetic phases  ...  This process can be explained by conformational shift occurring within the unfolded ensemble (U fi U 0 ), which is followed by the non-native intermediate (I) formation of this protein.  ...  In previous studies by Nakamura et al. using a lattice and an off-lattice protein model [6] [7] [8] , the existence of squeezed-exponential kinetics for protein folding was predicted.  ... 
doi:10.1016/j.febslet.2007.08.023 pmid:17761168 fatcat:t56xdk7mvjawfk6g2zp4hrj27a

The nature of protein folding pathways

S. Walter Englander, Leland Mayne
2014 Proceedings of the National Academy of Sciences of the United States of America  
These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process.  ...  How do proteins fold, and why do they fold in that way?  ...  Folding intermediates can be studied as significantly populated forms during kinetic folding, or as conformationally excited forms present at equilibrium under native conditions, or as equilibrium molten  ... 
doi:10.1073/pnas.1411798111 pmid:25326421 pmcid:PMC4234557 fatcat:g3hjio52ujfg7jjyhmamz326ai

Folding funnels, binding funnels, and protein function

Chung-Jung Tsai, Sandeep Kumar, Buyong Ma, Ruth Nussinov
1999 Protein Science  
Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding.  ...  The converse also holds: If kinetic and thermodynamic data are available, hints regarding the role of the protein and its binding selectivity may be obtained.  ...  This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-56000.  ... 
doi:10.1110/ps.8.6.1181 pmid:10386868 pmcid:PMC2144348 fatcat:pp3eti4gdnhzllxm7asvih4wgm

Structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein

C. Low, U. Weininger, P. Neumann, M. Klepsch, H. Lilie, M. T. Stubbs, J. Balbach
2008 Proceedings of the National Academy of Sciences of the United States of America  
As for p19 INK4d , equilibrium and kinetic folding analyses classify tANK to the family of sequential three-state folding proteins, with an unusual fast equilibrium between native and intermediate state  ...  Equilibrium and kinetic folding analyses of this protein by fluorescence and CD spectroscopy revealed a sequential three-state folding mechanism with the expected unusual fast equilibrium between the native  ...  Data deposition: The data reported in this paper have been deposited in the Protein Data Bank, www.pdb.org (PDB ID code 2RFM). ACKNOWLEDGMENTS.  ... 
doi:10.1073/pnas.0710657105 pmid:18305166 pmcid:PMC2268769 fatcat:3erx6s6yandofct73tjnrtqcfu
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