Minimal models for proteins and RNA from folding to function (Q37361859)

19 August 2017

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title

Minimal models for proteins and RNA from folding to function (English)

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19 August 2017

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19 August 2017

D Thirumalai

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19 August 2017

David L Pincus

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19 August 2017

Samuel S Cho

series ordinal

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19 August 2017

publication date

1 January 2008

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Progress in Molecular Biology and Translational Science

19 August 2017

published in

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19 August 2017

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19 August 2017

page(s)

203-250

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The chemical repertoire of natural ribozymes

19 August 2017

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Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2

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RNA folding: models and perspectives

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In vitro splicing of the ribosomal RNA precursor of tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence

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Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

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The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme

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Catalytic Activity of an RNA Molecule Prepared by Transcription in Vitro

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7 January 2021

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

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7 January 2021

Crystal structure of the ribosome at 5.5 A resolution

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7 January 2021

Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria

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7 January 2021

Beyond kinetic traps in RNA folding

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7 January 2021

Metal-binding sites in the major groove of a large ribozyme domain

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7 January 2021

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

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7 January 2021

Unusual mechanical stability of a minimal RNA kissing complex

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7 January 2021

Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway

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7 January 2021

Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid

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7 January 2021

A Single-Molecule Study of RNA Catalysis and Folding

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7 January 2021

Exploring the energy landscape of a small RNA hairpin

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7 January 2021

The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA

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7 January 2021

Kinetic intermediates in RNA folding

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7 January 2021

Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

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7 January 2021

Amino acid replacement that eliminates kinetic traps in the folding pathway of pancreatic trypsin inhibitor

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7 January 2021

The renormalization group and critical phenomena

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7 January 2021

Computer simulation of protein folding

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7 January 2021

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7 January 2021

Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach

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7 January 2021

Dynamics of Random Hydrophobic-Hydrophilic Copolymers with Implications for Protein Folding

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7 January 2021

An elementary mode coupling theory of random heteropolymer dynamics

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7 January 2021

Kinetics and thermodynamics of folding in model proteins

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7 January 2021

Optimal protein-folding codes from spin-glass theory

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7 January 2021

Polymer principles of protein calorimetric two-state cooperativity

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7 January 2021

Protein folding funnels: a kinetic approach to the sequence-structure relationship

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7 January 2021

Funnels, pathways, and the energy landscape of protein folding: a synthesis

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7 January 2021

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

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7 January 2021

Maximizing RNA folding rates: a balancing act.

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7 January 2021

Kinetic traps in lysozyme folding

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7 January 2021

A lattice statistical mechanics model of the conformational and sequence spaces of proteins

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7 January 2021

Principles of protein folding--a perspective from simple exact models.

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7 January 2021

Minimum energy compact structures of random sequences of heteropolymers

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7 January 2021

Factors governing the foldability of proteins

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7 January 2021

Emergence of Preferred Structures in a Simple Model of Protein Folding

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7 January 2021

Magic Numbers in Protein Structures

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7 January 2021

Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains

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7 January 2021

Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models

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7 January 2021

The disulfide folding pathway of BPTI

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7 January 2021

Kinetic role of a meta-stable native-like two-disulphide species in the folding transition of bovine pancreatic trypsin inhibitor

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7 January 2021

Conformational restrictions on the pathway of folding and unfolding of the pancreatic trypsin inhibitor

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7 January 2021

Reexamination of the folding of BPTI: predominance of native intermediates.

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7 January 2021

Kinetic role of nonnative species in the folding of bovine pancreatic trypsin inhibitor

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7 January 2021

Modeling the role of disulfide bonds in protein folding: Entropic barriers and pathways

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7 January 2021

Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor

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7 January 2021

Rapid formation of the native 14-38 disulfide bond in the early stages of BPTI folding.

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7 January 2021

Chaperonin-mediated protein folding

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7 January 2021

The nature of folded states of globular proteins

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7 January 2021

Probing the instabilities in the dynamics of helical fragments from mouse PrPC.

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7 January 2021

The origins of asymmetry in the folding transition states of protein L and protein G.

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7 January 2021

Topological frustration and the folding of interleukin-1 beta

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7 January 2021

Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics

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7 January 2021

Mechanisms and kinetics of beta-hairpin formation

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7 January 2021

Folding dynamics and mechanism of β-hairpin formation

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7 January 2021

Effects of crowding and confinement on the structures of the transition state ensemble in proteins

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7 January 2021

Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin

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7 January 2021

Crowded, cell-like environment induces shape changes in aspherical protein

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7 January 2021

Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back

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7 January 2021

Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations

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7 January 2021

Dynamics of allosteric transitions in GroEL.

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7 January 2021

Internal strain regulates the nucleotide binding site of the kinesin leading head

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7 January 2021

Mechanical control of the directional stepping dynamics of the kinesin motor

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7 January 2021

Mechanical unfolding of RNA hairpins

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7 January 2021

Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins

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7 January 2021

Mechanical unfolding of RNA: from hairpins to structures with internal multiloops

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7 January 2021

Reversible unfolding of single RNA molecules by mechanical force

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7 January 2021

Mechanical unfolding intermediates in titin modules.

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7 January 2021

Coarse-grained normal mode analysis in structural biology

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7 January 2021

Gaussian Dynamics of Folded Proteins

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7 January 2021

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

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7 January 2021

Exploring the energy landscape of GFP by single-molecule mechanical experiments

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7 January 2021

Extracting function from a beta-trefoil folding motif

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7 January 2021

Single-molecule studies of RNA polymerase: motoring along

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7 January 2021

The way things move: looking under the hood of molecular motor proteins

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7 January 2021

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

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7 January 2021

Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains

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7 January 2021

Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Allostery and cooperativity revisited

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

A novel brain ATPase with properties expected for the fast axonal transport motor

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7 January 2021

Identification of a novel force-generating protein, kinesin, involved in microtubule-based motility

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

X-ray Structure of Motor and Neck Domains from Rat Brain Kinesin,

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7 January 2021

The Crystal Structure of Dimeric Kinesin and Implications for Microtubule-Dependent Motility

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

15 A resolution model of the monomeric kinesin motor, KIF1A.

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7 January 2021

A structural change in the kinesin motor protein that drives motility

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Kinesin hydrolyses one ATP per 8-nm step

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Single kinesin molecules studied with a molecular force clamp

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Probing the kinesin reaction cycle with a 2D optical force clamp

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Kinesin moves by an asymmetric hand-over-hand mechanism

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Kinesin walks hand-over-hand

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Simple mechanochemistry describes the dynamics of kinesin molecules

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Kinesin crouches to sprint but resists pushing

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Molecular motors: a theorist's perspective

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7 January 2021

Kinesin's network of chemomechanical motor cycles.

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Backsteps induced by nucleotide analogs suggest the front head of kinesin is gated by strain

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Loading direction regulates the affinity of ADP for kinesin

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7 January 2021

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

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7 January 2021

Extracting stacking interaction parameters for RNA from the data set of native structures

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics

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7 January 2021

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Charge density of divalent metal cations determines RNA stability

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7 January 2021

Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations

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7 January 2021

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

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7 January 2021

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

RNA folding and unfolding

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7 January 2021

Stretching single-domain proteins: phase diagram and kinetics of force-induced unfolding

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Forced-unfolding and force-quench refolding of RNA hairpins

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

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https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

VMD: visual molecular dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: evidence for a kinetic partitioning mechanism.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6603%2808%2900406-6

7 January 2021

10.1016/S0079-6603(08)00406-6

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DOI

1 reference

19 August 2017

1 reference

1 reference