PROTEIN PHYSICS LECTURES 17-18

Slides:

Advertisements

Similar presentations

Jane Clarke May 2004 How do proteins withstand force? Examining the effect of force on a protein folding landscape by combining atomic force microscopy,

Advertisements

Computational methods in molecular biophysics (examples of solving real biological problems) EXAMPLE I: THE PROTEIN FOLDING PROBLEM Alexey Onufriev, Virginia.

Protein Denaturation FDSC400. Goals Denaturation Balance of forces Consequences of denaturation.

Protein Threading Zhanggroup Overview Background protein structure protein folding and designability Protein threading Current limitations.

1 PROTEINS. 2 Proteins Proteins are polymers made of monomers called amino acids (aka building blocks) 8-10 we can not make. All proteins are made of.

Folding and flexibility. Outline What is protein folding ? How proteins fold in vivo ? What is protein flexibility ?

CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Homology Modeling Anne Mølgaard, CBS, BioCentrum, DTU.

Determination of alpha-helix propensities within the context of a folded protein Blaber et al. J. Mol. Biol 1994.

Protein folding kinetics and more Chi-Lun Lee ( 李紀倫 ) Department of Physics National Central University.

Energetics and kinetics of protein folding. Comparison to other self-assembling systems?

AGR2451 Lecture 2 - M. Raizada -Pick-up questionnaire at the front; results from last week -Did you review your notes within 24 hours?? -15 minute meetings.

What are proteins? Proteins are important; e.g. for catalyzing and regulating biochemical reactions, transporting molecules, … Linear polymer chain composed.

Protein Secondary Structure Lecture 2/19/2003. Three Dimensional Protein Structures Confirmation: Spatial arrangement of atoms that depend on bonds and.

Bioinformatics: Practical Application of Simulation and Data Mining Protein Folding I Prof. Corey O’Hern Department of Mechanical Engineering & Materials.

Department of Mechanical Engineering

Operone lac Principles of protein structure and function Function is derived from structure Structure is derived from amino acid sequence Different.

Mrs. Einstein Research in Molecular Biology. Importance of proteins for cell function: Proteins are the end product of the central dogma YOU are your.

Part I : Introduction to Protein Structure A/P Shoba Ranganathan Kong Lesheng National University of Singapore.

PROTEIN PHYSICS LECTURES  In vivo folding  In vitro folding: spontaneously  Levinthal paradox: spontaneously - how?  Protein folding intermediates.

Conformational Entropy Entropy is an essential component in ΔG and must be considered in order to model many chemical processes, including protein folding,

Classwork II: NJ tree using MEGA. 1.Go to CDD webpage and retrieve alignment of cd00157 in FASTA format. 2.Import this alignment into MEGA and convert.

1 Proteins Protein functions include: 1. enzyme catalysts 2. defense 3. transport 4. support 5. motion 6. regulation 7. storage Chapter 3- part 2.

Tertiary Structure Globular proteins (enzymes, molecular machines)  Variety of secondary structures  Approximately spherical shape  Water soluble 

PROTEIN PHYSICS LECTURES 22-23

Introduction to Protein Structure Prediction BMI/CS 576 Colin Dewey Fall 2008.

Protein folding. A theoretical view Alexei Finkelstein Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia University.

PROTEIN PHYSICS LECTURE 21 Protein Structures: Kinetic Aspects (3)  Nucleation in the 1-st order phase transitions  Nucleation of protein folding  Solution.

Lecture 5 Web: pollev.com/ucibio Text: To: Type in:

PROTEIN FOLDING: H-P Lattice Model 1. Outline: Introduction: What is Protein? Protein Folding Native State Mechanism of Folding Energy Landscape Kinetic.

PROTEIN PHYSICS LECTURE 19 Protein Structures: Kinetic Aspects (1)  Basic facts on in vivo and in vitro folding: protein folds spontaneously protein folds.

Events in protein folding. Introduction Many proteins take at least a few seconds to fold, but almost all proteins undergo major structural transitions.

Rules 3 color cards= 3 Teams Team work + Individual Performance Highest scoring Team =Bonus marks to each team member In a team, each member will.

1 Proteins Proteins are polymers made of monomers called amino acids All proteins are made of 20 different amino acids linked in different orders Proteins.

Structural classification of Proteins SCOP Classification: consists of a database Family Evolutionarily related with a significant sequence identity Superfamily.

Protein Folding & Biospectroscopy Lecture 4 F14PFB David Robinson.

Conformat ional ENTROPY Sannali M Dittli 14 October 2015.

PROTEIN PHYSICS LECTURE 15. Protein Structures & Physical Background of Their Natural Selection  Structures  Selection.

Lecture 13 Protein Structure II Chapter 3. PROTEIN FOLDING.

CHM 708: MEDICINAL CHEMISTRY

Protein Folding.

Chapter 5 Proteins.

Protein Structure and Properties

Protein Structures: Thermodynamic Aspects (1)

Two views of the protein folding puzzle

Proteins Section 3.4.

Protein Denaturation FDSC400. Goals Denaturation Balance of forces Consequences of denaturation.

Enzymes How do catalysts speed up chemical reactions?

Basics of thermodynamics & kinetics

Introduction & overview

A Spring-loaded mechanism for the conformational change of Influenza Hemagglutinin Mani Foroohar.

Diverse Macromolecules

Liam M. Longo, Ozan S. Kumru, C. Russell Middaugh, Michael Blaber

PROTEIN PHYSICS LECTURES 22-23

Volume 108, Issue 3, Pages (February 2015)

Introduction to Biophysics Lecture 5 Proteins Structure

Understanding protein folding via free-energy surfaces from theory and experiment Aaron R Dinner, Andrej Šali, Lorna J Smith, Christopher M Dobson, Martin.

Volume 19, Issue 1, Pages (July 2005)

Foldability of a Natural De Novo Evolved Protein

by T. M. Jacobs, B. Williams, T. Williams, X. Xu, A. Eletsky, J. F

Chapter 3 Biological Molecules

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties Thomas Veitshans, Dmitri Klimov, Devarajan.

Linkage between ATP Consumption and Mechanical Unfolding during the Protein Processing Reactions of an AAA+ Degradation Machine Jon A. Kenniston, Tania.

Untangling the Influence of a Protein Knot on Folding

Introduction to Biophysics Lecture 17 Self assembly

Polymer Theory Why are we looking at polymer theory?

Volume 99, Issue 2, Pages (July 2010)

The Influence of Configurational Dependent Diffusion on Fast Protein Folding Dynamics Jin Wang, SUNY at Stony Brook 1. Diffusion coefficients versus Q.

Protein Structure.

Tural Aksel, Doug Barrick Biophysical Journal

Foldability of a Natural De Novo Evolved Protein

Presentation transcript:

PROTEIN PHYSICS LECTURES 17-18 Protein Structures: Thermodynamic aspects Unfolded proteins in vivo and in vitro Cooperative transitions of protein structures - Thermodynamic states of protein molecules Why protein denaturation is an “all-or-none” phase transition? “Energy gap” and “all-or-none” melting

Protein denaturation: cooperative transition solid protein structures can denaturate (decay), and then re-nature (fold) both in vivo (e.g., when protein is synthesized or transported through a membrane), and in vitro Protein denaturation: cooperative transition ---------------protein---------------             ? ?

transition

Denaturation: “all-or-none” transition For a melting unit: T0S1=E1 Transition: |G1|= |-S1T|= =E1|T/T0| >> kT0 Denaturation: “all-or-none” transition in small (single-domain) proteins (Privalov, 1969) ΔH0/NUMBmol melting unit 1 molecule

S/k >> 1 T0=E/S

“All-or-none” decay of native protein structure: Ensures reliability Solid native state, unfolded coil, “more compact molten state” and cooperative transitions between them “All-or-none” decay of native protein structure: Ensures reliability and robustness of protein functioning (Tanford, 1968; Ptitsyn et al., 1981)

Secondary structure Side chain packing IN VARIOUS STATES: Secondary structure Side chain packing unfolded native native

“all-or-none”

e PROTEIN FOLDING: current picture (Dobson, 2003) (MG)

Why protein denaturation is an “all-or-none” phase transition? Peculiarities of protein structure: - Unique fold; - Close packing; - Flexible side chains at rigid backbone - Side chains rotamers Impossible to create a pore to rotate only one side chain  energy gap

“All-or-none” melting: a result of the “energy gap” ~ ln[M(E)] Start of the side chain liberation ←[small M(E)] ____ IS THE GAP “NATURAL”?

The “energy gap” is: - necessary for unique protein structure “all-or-none” transition results from the “energy gap” Energy landscape The “energy gap” is: - necessary for unique protein structure - necessary for fool-proof protein action - necessary for fast folding - produced by very rare sequences gap

narrow energy gap GAP WIDTH: MAIN PROBLEM OF EXPERIMENTAL PROTEIN PHYSICS PHYSICAL ESTIMATE: =??? BIOLOGICAL ESTIMATE: 1 0F ~1010 (NOT 1 0F ~10100!) RANDOM SEQUENCES MAKES A “PROTEIN-LIKE” STRUCTURE (SOLID, WITH A SPECIFIC BINDING: PHAGE DISPLAY). THIS IMPLIES THAT DE ~ 20 kT0 E is small relatively to the meting energy H  100 kT0: narrow energy gap

Protein Structures: Thermodynamics Protein denaturation: cooperative and, moreover, an “all-or-none” transition in small proteins and separate domains. Solid native state, unfolded coil & “molten globule”. Why protein denaturation is an “all-or-none” phase transition? “Energy gap” and “all-or-none” melting. “Protein-like” heteropolymers. ?