[Paper Review] Effect of hydrogen bonds on protein stability

Valentino Bianco, Svilen Iskrov+1 more|arXiv (Cornell University)|Nov 16, 2010

Material Dynamics and Properties65 references3 citations

TL;DR

This study proposes a coarse-grained model of a water monolayer that captures hydrogen bond (HB) cooperativity and applies it to simulate protein stability under varying temperature and pressure. Using Monte Carlo simulations, the model reproduces elliptical stability regions in the P-T plane, demonstrating cold, hot, and pressure denaturation, as well as molten globule states, with HB network disruption as a key driver of unfolding.

ABSTRACT

The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density fluctuations of surface water, or the destabilization of hydrophobic contacts because of the displacement of water molecules inside the protein, as proposed for high pressures. However, it is clear that water plays a fundamental role in the process. Here, we review some models that have been proposed to give insight into this problem. Next we describe a coarse-grained model of a water monolayer that successfully reproduces the complex thermodynamics of water and compares well with experiments on proteins at low hydration level. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations. Our goal is to perform a step in the direction of understanding how the interplay of cooperativity of water and interfacial hydrogen bonds affects the protein stability and the unfolding.

Motivation & Objective

• To understand how interfacial hydrogen bonds and water cooperativity influence protein stability and unfolding.
• To develop a coarse-grained model of water monolayers that reproduces the complex thermodynamics of confined water.
• To simulate the folding-unfolding behavior of a hydrophobic homopolymer in contact with the water monolayer under varying T and P.
• To investigate the mechanisms of cold, pressure, and thermal denaturation in a unified framework.
• To validate the model against experimental phase behavior and identify the role of hydrogen bond networks in protein stability.

Proposed method

• Develop a coarse-grained model of a water monolayer that explicitly accounts for hydrogen bond (HB) cooperativity.
• Use mean-field calculations and Monte Carlo simulations to study the thermodynamic properties of the water monolayer.
• Extend the model to include a self-avoiding hydrophobic homopolymer as a simplified protein in contact with the water layer.
• Simulate the system across a range of temperature (T) and pressure (P) conditions to map stability regions.
• Analyze the number and orientation of hydrogen bonds (HBs) in the hydration shell during folding and unfolding transitions.
• Compare simulated phase diagrams and structural states (folded, molten globule, unfolded) with experimental observations and theoretical predictions.

Experimental results

Research questions

• RQ1 How does hydrogen bond cooperativity in confined water influence protein stability across temperature and pressure?
• RQ2 Can a coarse-grained water monolayer model reproduce the elliptical stability region observed in protein phase diagrams?
• RQ3 What is the role of water's hydrogen bond network in driving cold denaturation and pressure-induced unfolding?
• RQ4 How do fluctuations in the hydration shell's HB structure correlate with protein unfolding transitions?
• RQ5 To what extent does the model capture intermediate states such as the molten globule under varying thermodynamic conditions?

Key findings

• The model successfully reproduces an elliptical stability region in the P-T plane, consistent with experimental protein phase diagrams.
• Cold denaturation occurs when the number of hydrogen bonds in the hydration shell is drastically reduced, even at low temperatures.
• Pressure denaturation is linked to a reduction in hydrogen bond count and disruption of the HB network, especially at high pressures.
• The system exhibits a molten globule state at intermediate conditions, characterized by partial collapse and reduced but non-zero HBs.
• The axes of the elliptical stability region are tilted, matching theoretical expectations and experimental observations.
• The model captures the unfolding of the protein upon cooling, pressure increase, and temperature increase, confirming all three denaturation pathways.