Soft Matter Science     


Soft Matter Science - Protein Science

Protein Science

I. Protein Folding

Protein folding is one of the most fundamental mysteries of molecular biology. Recent advances in experimental techniques that probe proteins at different stages during the folding process have shed light on the nature of the physical mechanisms and relevant interactions that determine the kinetics of folding, binding, function, and thermodynamic stability. However, many of the details of protein folding pathways remain unknown. Computer simulations performed at various levels of complexity ranging from simple lattice models, models with continuum solvent, to all atom models with explicit solvent can be used to supplement experiment and fill in some of the gaps in our knowledge about folding pathways.

1. beta Hairpin

The C-terminal beta hairpin of protein G has received much attention recently on both the experimental and theoretical fronts since it is one of the smallest naturally occurring systems, which exhibits many features of a full size protein and also is a faster folder. We have carried out the first all-atom simulation to explore the free energy landscape of the beta hairpin in explicit water with the OPLSAA force field and periodic boundary condition using a highly parallel replica exchange method combined with an efficient molecular dynamics (MD) algorithm, Particle - Particle Particle - Mesh Ewald (P3ME)/reference system propagator algorithm (RESPA). A blend view of hydrophobic-core-centric and hydrogen-bond-centric folding mechanism was proposed from our simulation results.

2. Trp-cage

This same technique was also applied to study the folding free energy landscape in explicit water for Trp-cage, a 20-residue miniprotein, which is believed to be the fastest folding protein known so far and can serve to meet both ends of experimental and theoretical studies. Based on detailed results from the simulation in explicit solvent, a folding mechanism has been proposed for this Trp-cage that involves an intermediate state where the structures show two partially prepacked hydrophobic cores separated by a salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state might have provided a mechanism for a fast two-step folding process for this miniprotein.

Our rigorous studies of these proteins provide a foundation for investigating more complex proteins and suggest that more work needs to be done in the force field parameterization to yield the correct temperature dependence from simulations.

Related Publications:

  • R. H. Zhou,
    Trp-cage: Folding Free Energy Landscape in Explicit Water,
    Proc. Natl. Acad. Sci., 100, 13280-13285, 2003
  • R. H. Zhou, B. J. Berne and R. Germain,
    Free energy landscape of a beta-hairpin folding in explicit water,
    Proc. Natl. Acad. Sci. 98, 14931-14936, 2001

II. Protein Misfolding and Aggregation

Aside from being a fundamentally interesting problem, misfolding and aggregation of proteins have been implicated in many fatal diseases such as Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD) and mad cow disease and, as such, are the subject of great interest in molecular biology. Many researchers have suggested that misfolded beta-amyloid peptides play a crucial role in such diseases. When beta-amyloid peptides misfold, they may accumulate into fibrils and plaques. However, recent experiments pioneered by Dobson and coworkers have shown that amyloids and fibrils can be formed from almost any protein given the appropriate conditions, and lysozyme is a good example. This finding indicates that there are many other examples of mutation-induced misfolding, the exploration of which could yield insights into the mechanism of diseases caused by protein misfolding.

1. Lysozyme

In this project, we have used MD simulations to study how a single-point mutation (W62G) affects the stability and misfolding of the protein hen egg-white lysozyme. Both the wild-type and mutant lysozymes were simulated on a BlueGene/L supercomputer. Our results show that the mutant structure is indeed much less stable than the wild-type one, which is consistent with the recent urea denaturing experiment, and offer useful insights into the mechanism behind lysozyme protein misfolding and subsequent aggregation.

2. gamma-Crystallins

Human gamma D crystallin is the third most abundant gamma-crystallin in the lens and a significant component of the age-onset cataract. Characterization of cataractogenesis in the native environment has been difficult due to the physical integrity of the lens. The direct identification of the state of aggregation precursors within the lens fiber cells or the intact lens has not been achieved due to experimental complications. In this study, we used extensive atomistic molecular dynamics simulations to characterize unfolding of human gamma D crystallin followed by its oligomerization. This observation  is consistent with the current models of cataractogenesis. Mapping the initial pathways of crystallin aggregation can provide a route toward targeted searches for therapeutic agents inhibiting pathological deposition for a number of protein deposition diseases including those concerning cataract formation.

Related Publications:

  • P. Das, J. A. King, and R. H. Zhou,
    Aggregation of Partially Folded gamma-Crystallin Associated with Human Cataracts via Domain Swapping at the C-terminal beta-strands,
    Proc. Natl. Acad. Sci., 108, 10514-10519, 2011 (featured article)
  • R. H. Zhou, M. Eleftheriou, A. Royyuru, B. J. Berne,
    Destruction of long-range interactions by a single mutation in lysozyme,
    Proc. Natl. Acad. Sci., 104, 5824-5829, 2007

III. Nanoscale Dewetting in Physical and Biological Systems

Hydrophobicity is believed to be the main driving force in protein folding, a process that still remains a mystery. Understanding the nature of hydrophobic collapse is an important step towards solving the protein folding problem. For simple nanoscale solutes, such as paraffin-like plates, hydrophobicity induces a strong drying transition in the gap between the hydrophobic surfaces as they approach each other. This transition, although occurring on a microscopic scale, is analogous to a first order phase transition from liquid to vapor. The question we try to address in this project is whether or not a similar dewetting transition occurs when proteins fold or form large multi-protein complexes, and, if it does, what physical interactions govern the dewetting critical distance as well as the collapse speed. Such a deeper understanding might help (1) to design novel water nanopores (similar to membrane protein Aquaprion); (2) to design nanoscale molecular switches; and (3) to better understand the mechanism behind all subcellular self-assemblies.

To our surprise, we have recently observed such a dramatic dewetting transition inside a nanoscale channel of protein melittin tetramer. Melittin, a 26-residue polypeptide, is a small toxic protein found in honey bee venom, which often self-assembles into a tetramer. The strong dewetting transition occurs in a subnanosecond time scale and a subnanometer (up to 2-3 water diameters) length scale. The dewetting transition is also found to be very sensitive to single mutations of the three very hydrophobic amino acids (isoleucines) to less hydrophobic residues. Such mutations in the right locations can switch the channel from being dry to being wet - a "molecular switch". Thus quite subtle changes in hydrophobic surface topology can have a pronounced influence on the drying transition. This study shows that, even in the presence of the polar protein backbone, sufficiently hydrophobic protein surfaces can induce a liquid-vapor transition which can then provide an enormous driving force towards further collapse. Our early study also shows that the protein-water electrostatic forces are found to be largely responsible for the much slower collapse in the multi-domain protein than the idealized nanoscale hydrophobic plates, while the van der Waals interactions largely count for the smaller dewetting critical distances.

Related Publications:

  • P. Liu, X. Huang, R. Zhou and B. J. Berne,
    Drying and Hydrophobic Collapse of Melittin Tetramer,
    Nature, 437, 159-162, 2005
  • R. Zhou, X. Huang, C. Margulius and B. J. Berne,
    Hydrophobic Collapse in Multi-domain Protein Folding,
    Science, 305, 1605-1609, 2004










  • Otitoaleke G. Akinola
  • Matteo Castelli
  • Camilo Jimenez
  • Yuxing Peng
  • Michael Pitman
  • Raul Araya Secchi
  • Frank Suits
  • Jacinta Wubben
  • Zhen Xia
  • Payel Das