Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails

Pande VS (2010) Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Comput Biol 6(6): e1000829. doi:10.1371/journal.pcbi.1000829 Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails Peter M. Kasson 0 Erik Lindahl 0 Vijay S. Pande 0 Matthew P. Jacobson, University of California San Francisco, United States of America 0 1 Department of Chemistry, Stanford University, Stanford, California, United States of America, 2 Center for Biomembrane Research, Stockholm University , Stockholm , Sweden Membrane fusion is essential to both cellular vesicle trafficking and infection by enveloped viruses. While the fusion protein assemblies that catalyze fusion are readily identifiable, the specific activities of the proteins involved and nature of the membrane changes they induce remain unknown. Here, we use many atomic-resolution simulations of vesicle fusion to examine the molecular mechanisms for fusion in detail. We employ committor analysis for these million-atom vesicle fusion simulations to identify a transition state for fusion stalk formation. In our simulations, this transition state occurs when the bulk properties of each lipid bilayer remain in a lamellar state but a few hydrophobic tails bulge into the hydrophilic interface layer and make contact to nucleate a stalk. Additional simulations of influenza fusion peptides in lipid bilayers show that the peptides promote similar local protrusion of lipid tails. Comparing these two sets of simulations, we obtain a common set of structural changes between the transition state for stalk formation and the local environment of peptides known to catalyze fusion. Our results thus suggest that the specific molecular properties of individual lipids are highly important to vesicle fusion and yield an explicit structural model that could help explain the mechanism of catalysis by fusion proteins. - Funding: This work was supported by supercomputing awards SNIC 025/08-17 and CNS-0619926. Financial support includes a Berry fellowship to PMK, a CBR grant to PMK and EL, ERC, SSF, and VR grants to EL, NIH GM062868 to VSP, and a STINT collaborative grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Membrane fusion is critical to eukaryotic cell function; cells rely on fusion for vesicle trafficking and secretion, and viruses such as influenza and HIV utilize fusion to infect target cells. This poses a fundamental biophysical question: how do two lipid bilayers merge in a targeted manner without rupture, and how do proteins catalyze this process? Viruses in particular are faced with a host membrane not designed to be permissive to viral entry and must alter host membrane properties to achieve fusion. Simply bringing the viral and cellular membranes together is not sufficient for physiological fusion; mutagenesis experiments in influenza [1,2] and parainfluenza virus [3] have demonstrated that mutations to either the viral transmembrane anchor or the fusion peptide inserted in the host membrane can block fusion. In some cases [3], these mutations can be rescued by independently altering membrane properties, suggesting a direct connection between fusion peptides and lipid dynamics. The stalk model for membrane fusion proposes that proteins catalyze the formation of a series of lipidic fusion intermediates: the outer leaflets of each bilayer merge first, followed by opening of a fusion pore and merger of the inner leaflets [4]. There is strong indirect support for this model [48], and stalk structures have been observed in artificial model systems [9], but direct observation of fusion stalks in physiological membranes is extremely challenging due to their transient nature and small size. Molecular simulations provide an alternative way to study these processes and can also provide atomic detail of the fusion mechanism and transition state, yielding insight into the mechanism of biological catalysis of fusion. Vesicle fusion has previously been modeled with continuum approaches [8,1015] or coarse-grained simulation [1619], both of which have made important contributions to refining the stalk hypothesis and outlining fusion mechanisms. One previous highresolution simulation started from a pre-constructed stalk state, due to computational limitations, and examined a vesicle fusing to itself through a simulation boundary [20]. However, complete simulation of fusion in atomic detail has long been an important goal towards understanding atomic-level effects such as membrane dehydration and bilayer breakup upon stalk formation [21,22]. In cells, vesicle fusion is typically catalyzed by proteins. To understand the mechanism of this catalysis, we first wish to consider the biophysical nature of fusion, its transition state, and the surrounding molecular events. We have therefore performed atomic-resolution simulations both of complete vesicles fusing and of hemagglutinin fusion peptides interacting with lipid bilayers in order to examine the mechanism of vesicle fusion and especially stalk formation in more detail. The pathway for fusion that we observe in our simulations transits through stalk and hemifused intermediates largely as predicted by the stalk hypothesis, but we observe new high-resolution details important to understanding the transition state for stalk formation and thus how fusion proteins may catalyze the fusion process. To identify this transition state from simulations, we employ committor analysis [2325], a statistical means to evaluate the Membrane fusion is a common underlying process critical to neurotransmitter release, cellular trafficking, and infection by many viruses. Proteins have been identified that catalyze fusion, and mutations to these proteins have yielded important information on how fusion occurs. However, the precise mechanism by which membrane fusion begins is the subject of active investigation. We have used atomic-resolution simulations to model the process of vesicle fusion and to identify a transition state for the formation of an initial fusion stalk. Doing so required substantial technical advances in combining high-performance simulation and distributed computing to analyze the transition state of a complex reaction in a large system. The transition state we identify in our simulations involves specific structural changes by a few lipid molecules. We also simulate fusion peptides from influenza hemagglutinin and show that they promote the same structural changes as are required for fusion in our model. We therefore hypothesize that these changes to individual lipid molecules may explain a portion of the catalytic activity of fusion proteins such as influenza hemagglutinin. transition state (as well as the ful (...truncated)