Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Oleksandr Kokhan Project Name: protein_e-wire Division: CSE Project title: Solar energy conversion in biomimetic molecular architectures Associated funding: This project is supported by three funding programs within the DOE-BES Division of Chemical Sciences, Geosciences, and Biosciences: i) Solar Photochemistry; ii) Photosynthetic Systems; iii) Energy Frontier Research Center: Argonne Northwestern Solar En Other Systems: N/A Science: This computational project will supplement our experimental work on construction and characterization of water-splitting catalysts and biomimetic molecular architectures for solar energy conversion. The first aim is to continue to use all-atom Molecular Dynamics (MD) simulations to predict conformations and structural dynamics of several photosensitizers covalently linked to PpcA, a multi-heme c-type cytochrome from Geobacter sulfurreducens. These results will facilitate interpretation of photo-induced kinetic electron transfer rates, Circular Dichroism (CD) spectroscopy, Heteronuclear Single Quantum Correlation (HSQC) NMR data as well as Small- and Wide-Angle X-ray Scattering (SAXS, WAXS). This will provide an insight into strategies for optimization of electron transfer rates within biomimetic hybrids. The second aim is to use MD to simulate equilibrium positions and dynamics of mutations needed to tune redox potentials of PpcA hemes. Our third goal is to use MD simulations to predict and elucidate structural mechanisms of ligand-driven protein oligomerization. Finally, we will start a new project focused on understanding of inter-domain static and dynamic interactions in several multiheme cytochromes and how they effect electron transfer rates through these “molecular wires”. Project description: We are developing biomimetic molecular architectures for efficient solar energy conversion using artificial and natural photosensitizers combined with natural and genetically engineered host systems capable to support long-lived charge-separated states and conduct charges away from the photosensitizers. We recently developed and characterized a series of 22 cysteine mutants of PpcA, a multiheme redox protein from Geobacter sulfurreducens, which demonstrate picosecond photo-induced electron transfer rates. Further, at least 2 attachment sites showed negligible activation energy barriers resulting in similar apparent reaction rates at 2.7 and 295K. These are remarkable results considering that neither picosecond photo-induced electron transfer rates nor activationless reaction rates were observed in comparable synthetic systems, though they are common in natural photosynthesis. However, any attempts in understanding how and why our experimental system repl icates Nature will require detailed structural information in order to interpret the observed kinetic data and to guide our future developments. Solution-state NMR data confirms tightly folded globular shape. However, obtaining full atomic structures is challenging due to a number of paramagnetic centers within the constructs. Obtaining high quality crystals in order to solve structures of labeled PpcA mutants so far has been elusive. The molecular dynamics simulations of in silico mutation followed by validating computational data with experimental X-ray scattering work and HSQC NMR provide us with a valuable tool to visualize structural changes, generate hypotheses about the mechanisms and factors controlling charge transfer and to develop experimental testing approaches. In the past we have developed CHARMM force field parameters for several photosensitizers and obtained promising preliminary results for some of PpcA mutants in their oxidized form linked to Ru(bpy)3 which closely matched X-ray scattering data. In FY2018 one area of our work will be focused on simulations of 14 PpcA mutants which do not show significant perturbations and unfolding in SAXS data. We will perform simulations on NAMD 2.12 with the most recent CHARMM36m force field. The latter is different from CHARMM27 used in our previous work and should produce even more reliable results and accomplish this goal within FY2018 unlike previously simulations spanning multiple funding cycles and forcing to use outdated force fields. Based on our previous experience, we expect that triplicate 300-500 ns all-atom MD simulations of selected PpcA biohybrids with explicit solvent will provide sufficient sampling of protein conformational space and help us to better rationalize the colle cted kinetic data on charge transfer rates and SAXS/WAXS scattering profiles as well as the observed perturbations in the NMR data. At the initial stages of the project we will focus on the systems with all three PpcA hemes either oxidized. For most interesting cases, we will also perform simulations with all hemes reduced. This is particularly interesting as it results in a significant change of the total protein change from +4 to +1. All MD simulations will be performed with the standard for protein MD conditions: nPT, PME electrostatics, explicit TIP3 water boxes sufficiently large to keep interaction energy negligible between protein mirror images. Though the system is relatively small with about 14,000 atoms, our benchmarks on Bebop show that we have about 20% speed up (30ps/core hour) per core when simulations are run on 1 Broadwell node in comparison with our benchmarks on Blues. Overall, we expect to perform simulations of about 20 different biohybrids in triplicate for 400ns. This will require 800,000 core hours. The second major goal is to expand our work on tuning heme potentials and electron transfer pathways within cytochromes using PpcA as a model system and introducing mutations in the heme environment. The mutations will be selected based on our previous experimental work and will be used in conjunction with ongoing crystallographic studies performed in collaboration with Raj Pokkuluri (BIO). The system size and computational approach will be the same as above. We anticipate about 15 unique systems which will require approximately 600,000 core hours. Our third goal is to switch to most recent CHARMM force field and to perform triplicate simulations for 4 different proteins (cyt c, cyt c4, PpcA, lysozyme). We will continue to use simulations with 4 copies of proteins and 8 photosensitizers. Previously we found that this is a good trade-off between the size and ability to see complex formation with binding/unbinding events happening at the time scale of 30-80 ns and remarkably well matching NMR data for PpcA, the only system which was accessible with NMR spectroscopy. These systems have about 100-120,000 atoms. They scale better than 90% with up to 4 Broadwell nodes and produce 4.2 ps/core-hour. We plan to run these simulations for 300-500ns to observe multiple binding and unbinding events. We expect to use 1,150,000 core hours. Our last aim is to simulate interdomain interaction in 4 domain (ABCD), 12 –heme GSU-1996 cytochrome. The structures of this entire protein (ABCD domains) as well as 2-domain constructs (AB, BC, CD) have been previously determined with X-ray crystallography. However, it is nearly certain that crystal packing has affected interdomain interactions and does not show an accurate heme-heme distances and interfacial interactions. We plan to use all-atom MD in combination with solution-state SAXS to study solution-state behavior of this “biological wire” spanning more than 100Å. We will perform triplicated simulations of the entire protein (59,000 atoms, 7.7 ps/core-hour) and all three 2-domain constructs (23,000 atoms, 16 ps/core-hour) for 400 ns. This work will require 390,000 core-hours. This project will help us to understand interfacial interactions between domains and their implications for inter-domain electron transfer. This will also help us to understand the consequ ences of protein truncation on domain dynamics which will ultimately allow us to build direction electron transfer chains sufficiently long to stabilize charge separates states at time scales comparable to native photosynthesis. Industry partnership: Project URL: http://blogs.anl.gov/solar-energy/ Current FY Hours Used: undetermined amount New FY Requested allocation: 2940000 Q1: 735000 Q2: 735000 Q3: 735000 Q4: 735000 Justification: NAMD 2.12 is a highly scalable molecular dynamics simulations code. While we still working on optimization on Bebop, with our currently compiled MPI code we already see about 20% improvement per Broadwell core over our benchmarks on Blues. For simulations involving multiple nodes we see better than 95% scaling with ~1,000atoms/core and ~80% with ~400atoms/core with network latency becoming a bottleneck beyond that ratio. Storage requirements: Default 1TB will be sufficient Thank You, The LCRC Accounts System