Site-specific collapse dynamics guide the formation of the cytochrome c′ four-helix bundle

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Proceedings of the National Academy of Sciences of the United States of America

• Publication date

  2007-01-02

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1073/pnas.0609413103PMID 17179212PMCID PMC1765420
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Stability and folding kinetics of structurally characterized cytochrome c-b562.

  2006cited by this paper
• Dynamics, energetics, and structure in protein folding.

  2006cited by this paper
• Molecular dimensions and their distributions in early folding intermediates.

  2006cited by this paper
• Low barrier kinetics: Dependence on observables and free energy surface

  2006cited by this paper
• Role of unfolded state heterogeneity and en‐route ruggedness in protein folding kinetics

  2006cited by this paper
• Different secondary structure elements as scaffolds for protein folding transition states of two homologous four‐helix bundles

  2005cited by this paper
• Nature of the cytochrome c molten globule.

  2005cited by this paper
• Kinetics are probe-dependent during downhill folding of an engineered lambda6-85 protein.

  2005cited by this paper
• Snapshots of cytochrome c folding.

  2005cited by this paper
• Many faces of the unfolded state: conformational heterogeneity in denatured yeast cytochrome C.

  2005cited by this paper
• Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562.

  2005cited by this paper
• Kinetics of loop formation and breakage in the denatured state of iso-1-cytochrome c.

  2005cited by this paper
• Kinetics are probe-dependent during downhill folding of an engineered λ6–85 protein

  2005cited by this paper
• Ultra-fast barrier-limited folding in the peripheral subunit-binding domain family.

  2005cited by this paper
• A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments.

  2005cited by this paper
• An Obligatory Intermediate in the Folding Pathway of Cytochrome c552 from Hydrogenobacter thermophilus*

  2005cited by this paper
• Specific collapse followed by slow hydrogen-bond formation of beta-sheet in the folding of single-chain monellin.

  2005cited by this paper
• Determination of the folding transition states of barnase by using PhiI-value-restrained simulations validated by double mutant PhiIJ-values.

  2005cited by this paper
• Early events in the folding of four-helix-bundle heme proteins.

  2005cited by this paper
• A protein folding pathway with multiple folding intermediates at atomic resolution.

  2005cited by this paper
• Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin.

  2004cited by this paper
• Conformational properties of the iso-1-cytochrome C denatured state: dependence on guanidine hydrochloride concentration.

  2004cited by this paper
• Detection-dependent kinetics as a probe of folding landscape microstructure.

  2004cited by this paper
• The protein folding 'speed limit'.

  2004cited by this paper
• Folding, conformational changes, and dynamics of cytochromes C probed by NMR spectroscopy.

  2004cited by this paper
• Theory of protein folding.

  2004cited by this paper
• Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding.

  2003cited by this paper
• Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all‐atom molecular dynamics simulations with ϕ value restraints

  2003cited by this paper
• Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins.

  2003cited by this paper
• Contact order revisited: Influence of protein size on the folding rate

  2003cited by this paper
• Cloning, heterologous expression, and characterization of recombinant class II cytochromes c from Rhodopseudomonas palustris.

  2003cited by this paper
• Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein.

  2002cited by this paper
• Mapping the cytochrome C folding landscape.

  2002cited by this paper
• Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering

  2002cited by this paper
• Experimental Identification of Downhill Protein Folding

  2002cited by this paper
• Understanding protein folding with energy landscape theory Part II: Quantitative aspects

  2002cited by this paper
• Specific and nonspecific collapse in protein folding funnels.

  2002cited by this paper
• Understanding protein folding with energy landscape theory Part I: Basic concepts

  2002cited by this paper
• Structural features of cytochrome c′ folding intermediates revealed by fluorescence energy-transfer kinetics

  2002cited by this paper
• Hydrophobic core packing in the SH3 domain folding transition state

  2002cited by this paper
• Cytochrome c′ folding triggered by electron transfer: Fast and slow formation of four-helix bundles

  2001cited by this paper
• Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics

  2000cited by this paper
• Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics.

  2000cited by this paper
• Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach

  2000cited by this paper
• Measuring denatured state energetics: deviations from random coil behavior and implications for the folding of iso-1-cytochrome c.

  2000cited by this paper
• Conservation of folding pathways in evolutionarily distant globin sequences

  2000cited by this paper
• Critical role of β-hairpin formation in protein G folding

  2000cited by this paper
• The SH3-fold family: experimental evidence and prediction of variations in the folding pathways.

  2000cited by this paper
• Critical role of beta-hairpin formation in protein G folding.

  2000cited by this paper
• A surprising simplicity to protein folding

  2000cited by this paper
• Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding

  1999cited by this paper
• Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

  1999cited by this paper
• The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved

  1999cited by this paper
• Experiment and theory highlight role of native state topology in SH3 folding

  1999cited by this paper
• Exponential analysis in physical phenomena

  1999cited by this paper
• Interpreting the folding kinetics of helical proteins

  1999cited by this paper
• Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain.

  1998cited by this paper
• Contact order, transition state placement and the refolding rates of single domain proteins.

  1998cited by this paper
• Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules

  1998cited by this paper
• Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain

  1998cited by this paper
• Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure.

  1998cited by this paper
• Theory of protein folding: the energy landscape perspective.

  1997cited by this paper
• From Levinthal to pathways to funnels

  1997cited by this paper
• Different folding transition states may result in the same native structure

  1996cited by this paper
• Is burst hydrophobic collapse necessary for protein folding?

  1995cited by this paper
• Movement of the position of the transition state in protein folding.

  1995cited by this paper
• Kinetics of protein folding: Nucleation mechanism, time scales, and pathways

  1995cited by this paper
• Resonance energy transfer: methods and applications.

  1994cited by this paper
• Funnels, pathways, and the energy landscape of protein folding: A synthesis

  1994cited by this paper
• Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions

  1994cited by this paper
• Single versus parallel pathways of protein folding and fractional formation of structure in the transition state.

  1994cited by this paper
• Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding.

  1993cited by this paper
• The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding.

  1992cited by this paper
• Conformational studies of a peptide corresponding to a region of the C-terminus of ribonuclease A: implications as a potential chain-folding initiation site.

  1991cited by this paper
• Mapping the transition state and pathway of protein folding by protein engineering

  1989cited by this paper
• Simultaneous determination of intramolecular distance distributions and conformational dynamics by global analysis of energy transfer measurements.

  1989cited by this paper
• Solving least squares problems

  1976cited by this paper
• The preparation of guanidine hydrochloride.

  1972cited by this paper
• Statistical mechanics of chain molecules

  1970cited by this paper
• Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms

  year unknowncited by this paper

• Kinetics of protein-assisted nucleic acid interconversion monitored by transient time resolved fluorescence in microfluidic droplets

  2021cites this paper
• Applications of time-resolved spectroscopy for microenvironment sensing and biomolecular interactions studies

  2017cites this paper
• Sequential Closure of Loop Structures Forms the Folding Nucleus during the Refolding Transition of the Escherichia coli Adenylate Kinase Molecule.

  2016cites this paper
• Probing Microsecond Reactions with Microfluidic Mixers and TCSPC

  2015cites this paper
• Out-of-equilibrium biomolecular interactions monitored by picosecond fluorescence in microfluidic droplets.

  2014cites this paper
• Fast closure of long loops at the initiation of the folding transition of globular proteins studied by time-resolved FRET-based methods

  2014cites this paper
• Snapshots of a protein folding intermediate

  2013cites this paper
• Critical evaluation of the two-state model describing the equilibrium unfolding of the PI3K SH3 domain by time-resolved fluorescence resonance energy transfer.

  2013cites this paper
• Intrachain contact dynamics in unfolded cytochrome cb562.

  2013cites this paper
• Advances in turbulent mixing techniques to study microsecond protein folding reactions.

  2013cites this paper
• The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

  2013cites this paper
• Fluorescence picoseconde de complexes bio-moléculaires hors équilibre dans un écoulement microfluidique

  2013cites this paper
• Understanding protein unfolding from molecular simulations

  2012cites this paper
• How, when and why proteins collapse: the relation to folding.

  2012cites this paper
• 3.5 Characterization of the Denatured State

  2012cites this paper
• Geometric Parameters Defining the Structure of Proteins—Relation to Early-Stage Folding Step

  2011cites this paper
• Charge photoinjection in intercalated and covalently bound [Re(CO)3(dppz)(py)]+-DNA constructs monitored by time-resolved visible and infrared spectroscopy.

  2011cites this paper
• Direct visualization reveals dynamics of a transient intermediate during protein assembly

  2011cites this paper
• Manifestations of native topology in the denatured state ensemble of Rhodopseudomonas palustris cytochrome c'.

  2011influential citation
• Chapter 3 DNA-Mediated CT in Re-DNA Constructs Monitored by Time Resolved Infrared Spectroscopy

  2011cites this paper
• Unfolding four-helix bundles

  2011cites this paper
• Sequential Checkpoints Govern Substrate Selection During Cotranslational Protein Targeting

  2010cites this paper
• Early events in protein folding

  2009cites this paper
• Thermodynamics and kinetics of iso-1-cytochrome c denatured state

  2009cites this paper
• Collapse transition in proteins.

  2009cites this paper
• Early Closure of Loops in the Refolding of Adenylate Kinase: A Possible Key Role for Non Local Interactions in the Initial Folding Steps

  2009cites this paper
• Folding energy landscape of cytochrome cb562

  2009cites this paper
• Exploring the Electrostatic Landscape of Proteins with Tryptophan Fluorescence

  2009cites this paper
• Early closure of a long loop in the refolding of adenylate kinase: a possible key role of non-local interactions in the initial folding steps.

  2009cites this paper
• Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

  2008cites this paper
• Probing the cytochrome c' folding landscape.

  2007cites this paper