Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

Bachmann, Michael; Janke, Wolfhard

doi:10.1007/978-3-540-74029-2_8

Cited by 11 publications

(16 citation statements)

References 88 publications

(176 reference statements)

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“…The hydrophobic effect that causes the formation of a compact core of hydrophobic amino acids screened from the polar solvent by a shell of polar residues is expected to be the principal driving force towards the native, functional protein conformation. [3][4][5] Conformational transitions accompanying molecular structuring processes, however, exhibit similarities to thermodynamic phase transitions and it should thus be possible to characterize these transitions by means of a strongly reduced set of effective degrees of freedom, in close correspondence to order parameters that separate thermodynamic phases. Assuming that a single "order" parameter Q is sufficient to distinguish between two (pseudo)phases, its mean value…”

Section: Conformational Mechanics Of Proteinsmentioning

confidence: 99%

“…Such minimal models for proteins have indeed been introduced 3,4 and have proven useful in thermodynamic analyses of folding, adsorption, and aggregation of polymers and proteins. 2,[5][6][7][8] In the simplest approaches, 3,4 only two types of amino acids are considered: hydrophobic and polar residues. This is plausible as most of the H P P P H Fig.…”

Section: From Microscopic To Mesoscopic Modelingmentioning

confidence: 99%

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Conformational Transitions in Molecular Systems

Bachmann

Janke

2008

Path Integrals — New Trends and Perspectives

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Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

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Section: Conformational Mechanics Of Proteinsmentioning

confidence: 99%

Section: From Microscopic To Mesoscopic Modelingmentioning

confidence: 99%

Conformational Transitions in Molecular Systems

Bachmann

Janke

2008

Path Integrals — New Trends and Perspectives

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“…The answer would be "no", if conformational transitions accompanying molecular structure-formation processes indeed exhibit similarities to thermodynamic phase transitions, in which case it should be possible to reveal general, qualitative properties by analyses of suitably simplified models on mesoscopic scales [1,2].…”

Section: Introductionmentioning

confidence: 99%

“…However, from a physics point of view, one may ask: Is it really necessary at all to employ all-atom models, if one is interested in generic features of molecular mechanics which typically anyway requires a cooperative action of larger subunits (monomers)? The answer would be "no", if conformational transitions accompanying molecular structure-formation processes indeed exhibit similarities to thermodynamic phase transitions, in which case it should be possible to reveal general, qualitative properties by analyses of suitably simplified models on mesoscopic scales [1,2].…”

Section: Introductionmentioning

confidence: 99%

Mesoscopic Properties of Molecular Folding and Aggregation Processes

Bachmann¹,

Janke²

2008

AIP Conference Proceedings

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Abstract. Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative behavior of the molecular subunits lining up to build chainlike macromolecules. Proteins experience conformational transitions related to thermodynamic phase transitions. For chains of finite length, an important difference of crossovers between conformational (pseudo)phases is, however, that these transitions are typically rather smooth processes, i.e., thermodynamic activity is not necessarily signalized by strong entropic or energetic fluctuations. Nonetheless, in order to understand generic properties of molecular structureformation processes, the analysis of mesoscopic models from a statistical physics point of view enables first insights into the nature of conformational transitions in small systems. Here, we review recent results obtained by means of sophisticated generalized-ensemble computer simulations of minimalistic coarse-grained models.

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“…This may be depicted as a step-like potential which qualitatively corresponds to a Lennard-Jones interaction with large-distance cutoff. Such polymer models have been applied to a large variety of problems including protein folding (where depends on the type of interacting residues) and surface adsorption [11][12][13][14][15][16][17][18][19]. They provide a coarse-grained approximation to flexible Θ-polymers and are a suitable and very efficient way for studying generic properties of the collapse and freezing transitions for relatively long polymer chains.…”

mentioning

confidence: 99%

Polymers in disordered environments

Blavatska¹,

Fricke²,

Janke³

2014

Condens. Matter Phys.

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A brief review of our recent studies aiming at a better understanding of the scaling behaviour of polymers in disordered environments is given. The main emphasis is on a simple generic model where the polymers are represented by (interacting) self-avoiding walks and the disordered environment by critical percolation clusters. The scaling behaviour of the number of conformations and their average spatial extent as a function of the number of monomers and the associated critical exponents γ and ν are examined with two complementary approaches: numerical chain-growth computer simulations using the PERM algorithm and complete enumerations of all possible polymer conformations employing a recently developed very efficient exact counting method.

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Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

Cited by 11 publications

References 88 publications

Conformational Transitions in Molecular Systems

Conformational Transitions in Molecular Systems

Mesoscopic Properties of Molecular Folding and Aggregation Processes

Polymers in disordered environments

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