The Levinthal paradox: yesterday and today

Slides:



Advertisements
Similar presentations
CISC667, F05, Lec21, Liao1 CISC 467/667 Intro to Bioinformatics (Fall 2005) Protein Structure Prediction 3-Dimensional Structure.
Advertisements

Determination of the Interfacial Water Content in Protein-Protein Complexes from Free Energy Simulations Peter Monecke, Thorsten Borosch, Jürgen Brickmann,
Adaptation to Natural Binocular Disparities in Primate V1 Explained by a Generalized Energy Model Ralf M. Haefner, Bruce G. Cumming Neuron Volume 57, Issue.
How surgeons can find information online? Martin Hewitt International Journal of Surgery Volume 5, Issue 6, Pages (December 2007) DOI: /j.ijsu
Chapter 1: Definition and classification of CKD Kidney International Supplements Volume 3, Issue 1, Pages (January 2013) DOI: /kisup
National Guidelines for Nursing Delegation
Date of download: 1/6/2018 Copyright © ASME. All rights reserved.
High US Child Poverty: Explanations and Solutions
Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition experiments  Antônio F Pereira de Araújo,
Young Min Rhee, Vijay S. Pande  Biophysical Journal 
Numerical Study of the Entropy Loss of Dimerization and the Folding Thermodynamics of the GCN4 Leucine Zipper  Jorge Viñals, Andrzej Kolinski, Jeffrey.
Folding Pathways of Prion and Doppel
162. Stability of Polymer/Plasmid DNA Complexes In Vitro and In Vivo
Epidemiology of Myelodysplastic Syndromes
How Many Protein Sequences Fold to a Given Structure
Volume 106, Issue 8, Pages (April 2014)
The future of protein secondary structure prediction accuracy
Child Poverty: Definition and Measurement
3-Dimensional Structure
Michael T. Klann, Alexei Lapin, Matthias Reuss  Biophysical Journal 
Volume 96, Issue 5, Pages (March 2009)
NA  Journal of Thoracic Oncology 
Carol Beth Post, Christopher M. Dobson  Structure 
Understanding protein folding via free-energy surfaces from theory and experiment  Aaron R Dinner, Andrej Šali, Lorna J Smith, Christopher M Dobson, Martin.
Jean-Pierre Kocher, Martine Prévost, Shoshana J Wodak, Byungkook Lee 
Folding of the Protein Domain hbSBD
Meng Qin, Jian Zhang, Wei Wang  Biophysical Journal 
Volume 114, Issue 1, Pages (January 2018)
From Computer Simulations to Human Disease
Confessions of a journal junkie
Chapter 2 Demographics Journal of Obstetrics and Gynaecology Canada
Study of Heart and Renal Protection (SHARP)
Sanjin Marion, Carmen San Martín, Antonio Šiber  Biophysical Journal 
Community-acquired pneumonia: epidemiologic and clinical consideration
Low-technology approaches
Murat Çetinbaş, Eugene I. Shakhnovich  Biophysical Journal 
Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model  Leonid A Mirny, Victor Abkevich,
Ivan Coluzza, Daan Frenkel  Biophysical Journal 
Protein Folding: An unfolding story
Ariel Afek, Itamar Sela, Noa Musa-Lempel, David B. Lukatsky 
Archives of Physical Medicine and Rehabilitation 
An Effective Solvent Theory Connecting the Underlying Mechanisms of Osmolytes and Denaturants for Protein Stability  Apichart Linhananta, Shirin Hadizadeh,
Volume 69, Issue 12, Pages (June 2006)
Cell dynamics of folding in two-dimensional model proteins
Kinetic Analysis of the Thermal Stability of the Photosynthetic Reaction Center from Rhodobacter sphaeroides  Arwel V. Hughes, Paul Rees, Peter Heathcote,
AGEs in foods: Do they play a role in uremia?
Multiple Folding Pathways of the SH3 Domain
Organization news Archives of Physical Medicine and Rehabilitation
Peter Tiffin, Jeffrey Ross-Ibarra  Trends in Ecology & Evolution 
News & Notes Journal of Allergy and Clinical Immunology
Knee kinematic and kinetic modifications under body weight unloading during overground walking at a constant speed  A.G. Fischer, E.M. Debbi, A. Wolf 
Volume 55, Pages S3-S16 (June 1999)
Feng Ding, Douglas Tsao, Huifen Nie, Nikolay V. Dokholyan  Structure 
Pawel Gniewek, Andrzej Kolinski  Biophysical Journal 
Table of Contents Nurse Leader Volume 16, Issue 3, (June 2018)
Charles A. Herzog  Kidney International 
Appendix D – Survey Questionnaire
Archives of Physical Medicine and Rehabilitation 
Yongli Zhang, Junyi Jiao, Aleksander A. Rebane  Biophysical Journal 
Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders  Jeetain Mittal, Robert B. Best  Biophysical.
Volume 2, Issue 6, Pages (June 2017)
IP193. Controlled Compression Treatment With a Constant Resting Pressure and High Peak Working Pressure  Toby Lundh  Journal of Vascular Surgery  Volume.
Monte Carlo simulations of protein folding using inexact potentials: how accurate must parameters be in order to preserve the essential features of the.
Alice S. Whittemore, Jerry Halpern 
Amir Marcovitz, Yaakov Levy  Biophysical Journal 
Michael T. Klann, Alexei Lapin, Matthias Reuss  Biophysical Journal 
Volume 96, Issue 2, Pages L7-L9 (January 2009)
Mark A. Socinski, MD  Journal of Thoracic Oncology 
Genomewide Comparison of DNA Sequences between Humans and Chimpanzees
Evolution of Specificity in Protein-Protein Interactions
Presentation transcript:

The Levinthal paradox: yesterday and today Martin Karplus  Folding and Design  Volume 2, Pages S69-S75 (June 1997) DOI: 10.1016/S1359-0278(97)00067-9 Copyright © 1997 Terms and Conditions

Figure 1 Folding of a 27-bead heteropolymer on a cubic lattice at low temperature. (a) The average effective energy, E, as a function of Q, the fraction of native contacts; there are 28 in the native state, which is a 3 × 3 × 3 cube. (b) The average effective free energy, F, as a function of Q. Results adapted from Figure 4 of [42] at T = 0.7. Details of the definition and methods are given in [42]. Folding and Design 1997 2, S69-S75DOI: (10.1016/S1359-0278(97)00067-9) Copyright © 1997 Terms and Conditions

Figure 2 Folding of a 27-bead heteropolymer on a cubic lattice at high temperature. (a, b) See Figure 1 for explanation. The sharp peak in (b) near 0.9 appears to be an artefact of the lattice simulation. The same sequence as in Figure 1 was used except that the native state was stabilized by offsetting the energies of all 28 native contacts by a random number from a Gaussian distribution with a mean of 0.0–0.8 kBT and a standard deviation of 0.1 kBT; T = 2. Folding and Design 1997 2, S69-S75DOI: (10.1016/S1359-0278(97)00067-9) Copyright © 1997 Terms and Conditions

Figure 3 Arrhenius plot of the folding reaction rate constant as a function of tempretature of the sequence used in Figure 1. Folding and Design 1997 2, S69-S75DOI: (10.1016/S1359-0278(97)00067-9) Copyright © 1997 Terms and Conditions