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Protein Folding and Interaction

Posted on: 2022-01-16 13:01

A. Protein folding, 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) γ-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.

B. Biological dewetting at scale of nanoscale

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.

C. Modeling Huntingtin Protein for HD

Huntington’s disease (HD) is caused by the mutational extension of nucleotide CAG repeats, which encode an elongated polyglutamine (polyQ), within the first exon of the Huntingtin (Htt) gene [1]. In adult onset HD, pathogenic threshold Q-length is between 36 and 40, with individuals with fewer repeats showing no disease activity. The strong correlation between increased CAG repeats in Htt and the development of HD was also confirmed by mouse models as well as in vitro experiments. Notwithstanding the well-established negative correlation between the length of polyQ and the onset age of HD, the mechanism by which expanded polyQ tracts cause dysfunction of neurons and lead to cell death is still unclear. Thus, a systematic study on how the polyQ-length affects the Htt protein structure, dynamics and its interaction with others is critical. We are currently using extensive all-atom molecular dynamics (MD) simulations of the full exon-1 of Htt with various polyQ-lengths to investigate the structural and polymeric properties of wtHtt (Q22) and mtHtt (other Q-lengths) that may trigger the formation of HD-related protein aggregates.
There exists strong correlation between the extended polyglutamines (polyQ) within exon-1 of Huntingtin protein (Htt) and age onset of Huntington’s disease (HD); however, the underlying molecular mechanism is still poorly understood. Here we apply extensive molecular dynamics simulations to study the folding of Htt-exon-1 across five different polyQ-lengths. We find an increase in secondary structure motifs at longer Q-lengths, including β-sheet content that seems to contribute to the formation of increasingly compact structures. More strikingly, these longer Q-lengths adopt supercompact structures as evidenced by a surprisingly small power-law scaling exponent (0.22) between the radius-of-gyration and Q-length that is substantially below expected values for compact globule structures (∼0.33) and unstructured proteins (∼0.50). Hydrogen bond analyses further revealed that the supercompact behavior of polyQ is mainly due to the “glue-like” behavior of glutamine’s side chains with significantly more side chain-side chain H-bonds than regular proteins in the Protein Data Bank (PDB). The orientation of the glutamine side chains also tend to be “buried” inside, explaining why polyQ domains are insoluble on their own.

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
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

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Institute of Quantitative Biology, Zhejiang University
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