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1. Author Correction: Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

Author

Shrestha, Rebika, Carpenter, Timothy S., Van, Que N., Agamasu, Constance, Tonelli, Marco, Aydin, Fikret, Chen, De, Gulten, Gulcin, Glosli, James N., López, Cesar A., Oppelstrup, Tomas, Neale, Chris, Gnanakaran, Sandrasegaram, Gillette, William K., Ingólfsson, Helgi I., Lightstone, Felice C., Stephen, Andrew G., Streitz, Frederick H., Nissley, Dwight V., and Turbyville, Thomas J.

Published
2024
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2. Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

Author

Shrestha, Rebika, Carpenter, Timothy S., Van, Que N., Agamasu, Constance, Tonelli, Marco, Aydin, Fikret, Chen, De, Gulten, Gulcin, Glosli, James N., López, Cesar A., Oppelstrup, Tomas, Neale, Chris, Gnanakaran, Sandrasegaram, Gillette, William K., Ingólfsson, Helgi I., Lightstone, Felice C., Stephen, Andrew G., Streitz, Frederick H., Nissley, Dwight V., and Turbyville, Thomas J.

Published
2024
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4. Arbitrarily accurate representation of atomistic dynamics via Markov Renewal Processes

Author

Agarwal, Animesh, Gnanakaran, Sandrasegaram, Hengartner, Nicholas, Voter, Arthur F., and Perez, Danny

Subjects
Condensed Matter - Statistical Mechanics
Abstract

Atomistic simulations with methods such as molecular dynamics are extremely powerful tools to understand nanoscale dynamical behavior. The resulting trajectories, by the virtue of being embedded in a high-dimensional configuration space, can however be difficult to analyze and interpret. This makes low-dimensional representations, especially in terms of discrete jump processes, extremely valuable. This simplicity however usually comes at the cost of accuracy, as tractable representations often entail simplifying assumptions that are not guaranteed to be realized in practice. In this paper, we describe a discretization scheme for continuous trajectories that enables an arbitrarily accurate representation in terms of a Markov Renewal Process over a discrete state space. The accuracy of the model converges exponentially fast as a function of a continuous parameter that has the interpretation of a local correlation time of the dynamics.

Published
2020

5. HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens

Author

Fischer, Will, Giorgi, Elena E, Chakraborty, Srirupa, Nguyen, Kien, Bhattacharya, Tanmoy, Theiler, James, Goloboff, Pablo A, Yoon, Hyejin, Abfalterer, Werner, Foley, Brian T, Tegally, Houriiyah, San, James Emmanuel, de Oliveira, Tulio, Africa, Network for Genomic Surveillance in South, Wilkinson, Eduan, Msomi, Nokukhanya, Iranzadeh, Arash, Fonseca, Vagner, Doolabh, Deelan, Mlisana, Koleka, von Gottberg, Anne, Walaza, Sibongile, Allam, Mushal, Ismail, Arshad, Mohale, Thabo, Glass, Allison J, Engelbrecht, Susan, Van Zyl, Gert, Preiser, Wolfgang, Petruccione, Francesco, Sigal, Alex, Hardie, Diana, Marais, Gert, Hsiao, Marvin, Korsman, Stephen, Davies, Mary-Ann, Tyers, Lynn, Mudau, Innocent, York, Denis, Maslo, Caroline, Goedhals, Dominique, Abrahams, Shareef, Laguda-Akingba, Oluwakemi, Alisoltani-Dehkordi, Arghavan, Godzik, Adam, Wibmer, Constantinos Kurt, Sewell, Bryan Trevor, Lourenço, José, Pond, Sergei L Kosakovsky, Weaver, Steven, Giovanetti, Marta, Alcantara, Luiz Carlos Junior, Martin, Darren, Bhiman, Jinal N, Williamson, Carolyn, Gnanakaran, Sandrasegaram, and Korber, Bette

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Pneumonia, Vaccine Related, Emerging Infectious Diseases, Prevention, Genetics, Lung, HIV/AIDS, Infectious Diseases, Infection, Good Health and Well Being, COVID-19, Evolution, Molecular, Genome, Viral, HIV-1, Humans, Immune Evasion, Mutation, Pandemics, Receptors, Virus, Recombination, Genetic, SARS-CoV-2, Selection, Genetic, Spike Glycoprotein, Coronavirus, Viral Proteins, Network for Genomic Surveillance in South Africa, evolution, glycosylation, immune escape, insertions and deletions, recombination, Microbiology, Immunology, Biochemistry and cell biology, Medical microbiology
Abstract

Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.

Published
2021

6. A coarse-grained model for synergistic action of multiple enzymes on cellulose

Author

Asztalos Andrea, Daniels Marcus, Sethi Anurag, Shen Tongye, Langan Paul, Redondo Antonio, and Gnanakaran Sandrasegaram

Subjects
Cellulose degradation, Synergy, Exo-cellulase, Endo-cellulase, Agent-based model, Spatial heterogeneity, Fuel, TP315-360, Biotechnology, TP248.13-248.65
Abstract

Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.

Published
2012
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7. Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus

Author

Zhao, Fangzhu, Berndsen, Zachary T., Pedreño-Lopez, Nuria, Burns, Alison, Allen, Joel D., Barman, Shawn, Lee, Wen-Hsin, Chakraborty, Srirupa, Gnanakaran, Sandrasegaram, Sewall, Leigh M., Ozorowski, Gabriel, Limbo, Oliver, Song, Ge, Yong, Peter, Callaghan, Sean, Coppola, Jessica, Weisgrau, Kim L., Lifson, Jeffrey D., Nedellec, Rebecca, Voigt, Thomas B., Laurino, Fernanda, Louw, Johan, Rosen, Brandon C., Ricciardi, Michael, Crispin, Max, Desrosiers, Ronald C., Rakasz, Eva G., Watkins, David I., Andrabi, Raiees, Ward, Andrew B., Burton, Dennis R., and Sok, Devin

Published
2022
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8. Visualization of the HIV-1 Env glycan shield across scales

Author

Berndsen, Zachary T., Chakraborty, Srirupa, Wang, Xiaoning, Cottrell, Christopher A., Torres, Jonathan L., Diedrich, Jolene K., López, Cesar A., Yates, John R., van Gils, Marit J., Paulson, James C., Gnanakaran, Sandrasegaram, and Ward, Andrew B.

Published
2020

9. Improving pandemic influenza risk assessment.

Author

Russell, Colin A, Kasson, Peter M, Donis, Ruben O, Riley, Steven, Dunbar, John, Rambaut, Andrew, Asher, Jason, Burke, Stephen, Davis, C Todd, Garten, Rebecca J, Gnanakaran, Sandrasegaram, Hay, Simon I, Herfst, Sander, Lewis, Nicola S, Lloyd-Smith, James O, Macken, Catherine A, Maurer-Stroh, Sebastian, Neuhaus, Elizabeth, Parrish, Colin R, Pepin, Kim M, Shepard, Samuel S, Smith, David L, Suarez, David L, Trock, Susan C, Widdowson, Marc-Alain, George, Dylan B, Lipsitch, Marc, and Bloom, Jesse D

Subjects
Humans, Influenza A virus, Risk Assessment, Public Health, Base Sequence, Geography, Models, Biological, Influenza, Human, Biological Evolution, Pandemics, Epidemiological Monitoring, emergence, evolutionary biology, genomics, human, infectious disease, influenza, microbiology, pandemic, viruses, Models, Biological, Influenza, Human, Biochemistry and Cell Biology
Abstract

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

Published
2014

10. High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope

Author

Mopuri, Rohini, primary, Welbourn, Sarah, additional, Charles, Tysheena, additional, Ralli-Jain, Pooja, additional, Rosales, David, additional, Burton, Samantha, additional, Aftab, Areeb, additional, Karunakaran, Kirti, additional, Pellegrini, Kathryn, additional, Kilembe, William, additional, Karita, Etienne, additional, Gnanakaran, Sandrasegaram, additional, Upadhyay, Amit A., additional, Bosinger, Steven E., additional, and Derdeyn, Cynthia A., additional

Published
2023
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11. Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Author

Hackl, Markus, primary, Contrada, Edward V., additional, Ash, Jonathan E., additional, Kulkarni, Atharv, additional, Yoon, Jinho, additional, Cho, Hyeon-Yeol, additional, Lee, Ki-Bum, additional, Yarbrough, John M., additional, López, Cesar A., additional, Gnanakaran, Sandrasegaram, additional, and Chundawat, Shishir P. S., additional

Published
2022
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12. Exploring CRD mobility during RAS/RAF engagement at the membrane

Author

Nguyen, Kien, primary, López, Cesar A., additional, Neale, Chris, additional, Van, Que N., additional, Carpenter, Timothy S., additional, Di Natale, Francesco, additional, Travers, Timothy, additional, Tran, Timothy H., additional, Chan, Albert H., additional, Bhatia, Harsh, additional, Frank, Peter H., additional, Tonelli, Marco, additional, Zhang, Xiaohua, additional, Gulten, Gulcin, additional, Reddy, Tyler, additional, Burns, Violetta, additional, Oppelstrup, Tomas, additional, Hengartner, Nick, additional, Simanshu, Dhirendra K., additional, Bremer, Peer-Timo, additional, Chen, De, additional, Glosli, James N., additional, Shrestha, Rebika, additional, Turbyville, Thomas, additional, Streitz, Frederick H., additional, Nissley, Dwight V., additional, Ingólfsson, Helgi I., additional, Stephen, Andrew G., additional, Lightstone, Felice C., additional, and Gnanakaran, Sandrasegaram, additional

Published
2022
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14. DOE/NCI Pilot 2: Molecular Determinants of Cancer

Author

Neale, Christopher Andrew, primary, Hettige, Jeevapani Jayaranga, additional, Gnanakaran, Sandrasegaram, additional, Garcia, Angel Enrique, additional, Lopez Bautista, Cesar Augusto, additional, Travers, Timothy, additional, and Agarwal, Animesh, additional

Published
2019
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16. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

Author

López, Cesar A., primary, Zhang, Xiaohua, additional, Aydin, Fikret, additional, Shrestha, Rebika, additional, Van, Que N., additional, Stanley, Christopher B., additional, Carpenter, Timothy S., additional, Nguyen, Kien, additional, Patel, Lara A., additional, Chen, De, additional, Burns, Violetta, additional, Hengartner, Nicolas W., additional, Reddy, Tyler J. E., additional, Bhatia, Harsh, additional, Di Natale, Francesco, additional, Tran, Timothy H., additional, Chan, Albert H., additional, Simanshu, Dhirendra K., additional, Nissley, Dwight V., additional, Streitz, Frederick H., additional, Stephen, Andrew G., additional, Turbyville, Thomas J., additional, Lightstone, Felice C., additional, Gnanakaran, Sandrasegaram, additional, Ingólfsson, Helgi I., additional, and Neale, Chris, additional

Published
2022
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17. A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence

Author

Welbourn, Sarah, primary, Chakraborty, Srirupa, additional, Yang, Jie E., additional, Gleinich, Anne S., additional, Gangadhara, Sailaja, additional, Khan, Salar, additional, Ferrebee, Courtney, additional, Yagnik, Bhrugu, additional, Burton, Samantha, additional, Charles, Tysheena, additional, Smith, S. Abigail, additional, Williams, Danielle, additional, Mopuri, Rohini, additional, Upadhyay, Amit A., additional, Thompson, Justin, additional, Price, Matt A., additional, Wang, Shiyu, additional, Qin, Zhaohui, additional, Shen, Xiaoying, additional, Williams, LaTonya D., additional, Eisel, Nathan, additional, Peters, Tiffany, additional, Zhang, Lu, additional, Kilembe, William, additional, Karita, Etienne, additional, Tomaras, Georgia D., additional, Bosinger, Steven E., additional, Amara, Rama R., additional, Azadi, Parastoo, additional, Wright, Elizabeth R., additional, Gnanakaran, Sandrasegaram, additional, and Derdeyn, Cynthia A., additional

Published
2022
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19. Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus

Author

Zhao, Fangzhu, primary, Berndsen, Zachary T., additional, Pedreño-Lopez, Nuria, additional, Burns, Alison, additional, Allen, Joel D., additional, Barman, Shawn, additional, Lee, Wen-Hsin, additional, Chakraborty, Srirupa, additional, Gnanakaran, Sandrasegaram, additional, Sewall, Leigh M., additional, Ozorowski, Gabriel, additional, Limbo, Oliver, additional, Song, Ge, additional, Yong, Peter, additional, Callaghan, Sean, additional, Weisgrau, Kim L., additional, Lifson, Jeffrey D., additional, Nedellec, Rebecca, additional, Voigt, Thomas B, additional, Laurino, Fernanda, additional, Louw, Johan, additional, Rosen, Brandon C., additional, Ricciardi, Michael, additional, Crispin, Max, additional, Desrosiers, Ronald C., additional, Rakasz, Eva G., additional, Watkins, David I., additional, Andrabi, Raiees, additional, Ward, Andrew B., additional, Burton, Dennis R., additional, and Sok, Devin, additional

Published
2021
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20. Generalizable coordination of large multiscale workflows

Author

Bhatia, Harsh, primary, Di Natale, Francesco, additional, Moon, Joseph Y., additional, Zhang, Xiaohua, additional, Chavez, Joseph R., additional, Aydin, Fikret, additional, Stanley, Chris, additional, Oppelstrup, Tomas, additional, Neale, Chris, additional, Schumacher, Sara Kokkila, additional, Ahn, Dong H., additional, Herbein, Stephen, additional, Carpenter, Timothy S., additional, Gnanakaran, Sandrasegaram, additional, Bremer, Peer-Timo, additional, Glosli, James N., additional, Lightstone, Felice C., additional, and Ingólfsson, Helgi I., additional

Published
2021
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23. SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines

Author

Shen, Xiaoying, primary, Tang, Haili, additional, McDanal, Charlene, additional, Wagh, Kshitij, additional, Fischer, William, additional, Theiler, James, additional, Yoon, Hyejin, additional, Li, Dapeng, additional, Haynes, Barton F., additional, Sanders, Kevin O., additional, Gnanakaran, Sandrasegaram, additional, Hengartner, Nick, additional, Pajon, Rolando, additional, Smith, Gale, additional, Glenn, Gregory M., additional, Korber, Bette, additional, and Montefiori, David C., additional

Published
2021
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26. Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III

Author

Chundawat, Shishir P.S., primary, Nemmaru, Bhargava, additional, Hackl, Markus, additional, Brady, Sonia K., additional, Hilton, Mark A., additional, Johnson, Madeline M., additional, Chang, Sungrok, additional, Lang, Matthew J., additional, Huh, Hyun, additional, Lee, Sang-Hyuk, additional, Yarbrough, John M., additional, López, Cesar A., additional, and Gnanakaran, Sandrasegaram, additional

Published
2021
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27. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

Author

Korber, Bette, primary, Fischer, Will M., additional, Gnanakaran, Sandrasegaram, additional, Yoon, Hyejin, additional, Theiler, James, additional, Abfalterer, Werner, additional, Hengartner, Nick, additional, Giorgi, Elena E., additional, Bhattacharya, Tanmoy, additional, Foley, Brian, additional, Hastie, Kathryn M., additional, Parker, Matthew D., additional, Partridge, David G., additional, Evans, Cariad M., additional, Freeman, Timothy M., additional, de Silva, Thushan I., additional, McDanal, Charlene, additional, Perez, Lautaro G., additional, Tang, Haili, additional, Moon-Walker, Alex, additional, Whelan, Sean P., additional, LaBranche, Celia C., additional, Saphire, Erica O., additional, Montefiori, David C., additional, Angyal, Adrienne, additional, Brown, Rebecca L., additional, Carrilero, Laura, additional, Green, Luke R., additional, Groves, Danielle C., additional, Johnson, Katie J., additional, Keeley, Alexander J., additional, Lindsey, Benjamin B., additional, Parsons, Paul J., additional, Raza, Mohammad, additional, Rowland-Jones, Sarah, additional, Smith, Nikki, additional, Tucker, Rachel M., additional, Wang, Dennis, additional, and Wyles, Matthew D., additional

Published
2020
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30. A massively parallel infrastructure for adaptive multiscale simulations

Author

Di Natale, Francesco, primary, Bhatia, Harsh, additional, Carpenter, Timothy S., additional, Neale, Chris, additional, Kokkila-Schumacher, Sara, additional, Oppelstrup, Tomas, additional, Stanton, Liam, additional, Zhang, Xiaohua, additional, Sundram, Shiv, additional, Scogland, Thomas R. W., additional, Dharuman, Gautham, additional, Surh, Michael P., additional, Yang, Yue, additional, Misale, Claudia, additional, Schneidenbach, Lars, additional, Costa, Carlos, additional, Kim, Changhoan, additional, D'Amora, Bruce, additional, Gnanakaran, Sandrasegaram, additional, Nissley, Dwight V., additional, Streitz, Fred, additional, Lightstone, Felice C., additional, Bremer, Peer-Timo, additional, Glosli, James N., additional, and Ingólfsson, Helgi I., additional

Published
2019
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38. Evolution of a family ofN-acetylglucosamine binding proteins containing the disulfide-rich domain of wheat germ agglutinin

Author

Gnanakaran Sandrasegaram, H. Tonie Wright, and Christine S. Wright

Subjects
Models, Molecular, EGF-like domain, Protein Conformation, Wheat Germ Agglutinins, Molecular Sequence Data, Protein domain, Sequence alignment, Biology, Genes, Plant, Poaceae, Acetylglucosamine, Protein structure, EVH1 domain, Lectins, Sequence Homology, Nucleic Acid, Genetics, Amino Acid Sequence, Molecular Biology, Peptide sequence, Ecology, Evolution, Behavior and Systematics, Binding Sites, Base Sequence, Molecular Structure, Oryza, Biological Evolution, Biochemistry, Cyclic nucleotide-binding domain, DEP domain, Plant Lectins, Sequence Alignment
Abstract

A disulfide-rich domain, first identified in wheat germ agglutinin, has now been identified in the amino acid and DNA sequences of a large number of other chitin-binding proteins. This 43-residue domain includes eight disulfide-linked cysteines and has been implicated in the binding of N-acetylglucosamine and its polymers. This study used 12 complementary DNA sequences and 1 amino acid sequence of proteins with one, two, and four copies of this domain to infer a 44-amino acid residue ancestor sequence for this domain, and to derive an evolutionary tree relating these domains in the different proteins. The tree relating these single-domain sequences is divided into two major branches, one consisting of the multidomain dimeric lectins, which we have earlier suggested arose by duplication of a single copy of the disulfide-rich domain, and the other branch consisting of the monomeric chitinases and wound-inducible proteins, which have a single copy of the domain fused to a larger polypeptide. Reference to the three-dimensional structure of WGA and its saccharide complexes shows that the saccharide-binding residues as well as cysteine and glycine residues are conserved among all available sequences. In contrast, many residues at the dimer interface of the domains of WGA are not conserved in those proteins with a single domain, implying that the aggregation state of the domains in these proteins differs from that of the gras lectins. Also, the base compositions of the four-domain and one-domain branches of the tree differ, indicating distinct selective pressures at the level of both protein structure and the gene or its transcript.

Published
1991

39. Improving pandemic influenza risk assessment

Author

Russell, Colin A, primary, Kasson, Peter M, additional, Donis, Ruben O, additional, Riley, Steven, additional, Dunbar, John, additional, Rambaut, Andrew, additional, Asher, Jason, additional, Burke, Stephen, additional, Davis, C Todd, additional, Garten, Rebecca J, additional, Gnanakaran, Sandrasegaram, additional, Hay, Simon I, additional, Herfst, Sander, additional, Lewis, Nicola S, additional, Lloyd-Smith, James O, additional, Macken, Catherine A, additional, Maurer-Stroh, Sebastian, additional, Neuhaus, Elizabeth, additional, Parrish, Colin R, additional, Pepin, Kim M, additional, Shepard, Samuel S, additional, Smith, David L, additional, Suarez, David L, additional, Trock, Susan C, additional, Widdowson, Marc-Alain, additional, George, Dylan B, additional, Lipsitch, Marc, additional, and Bloom, Jesse D, additional

Published
2014
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40. Author response: Improving pandemic influenza risk assessment

Author

Russell, Colin A, primary, Kasson, Peter M, additional, Donis, Ruben O, additional, Riley, Steven, additional, Dunbar, John, additional, Rambaut, Andrew, additional, Asher, Jason, additional, Burke, Stephen, additional, Davis, C Todd, additional, Garten, Rebecca J, additional, Gnanakaran, Sandrasegaram, additional, Hay, Simon I, additional, Herfst, Sander, additional, Lewis, Nicola S, additional, Lloyd-Smith, James O, additional, Macken, Catherine A, additional, Maurer-Stroh, Sebastian, additional, Neuhaus, Elizabeth, additional, Parrish, Colin R, additional, Pepin, Kim M, additional, Shepard, Samuel S, additional, Smith, David L, additional, Suarez, David L, additional, Trock, Susan C, additional, Widdowson, Marc-Alain, additional, George, Dylan B, additional, Lipsitch, Marc, additional, and Bloom, Jesse D, additional

Published
2014
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44. Role of solvent on chemical reaction dynamics of small molecules

Author

Gnanakaran, Sandrasegaram and Gnanakaran, Sandrasegaram

Abstract

For this thesis work, equilibrium (EMD) and non-equilibrium (NEMD) molecular dynamics simulations have been used to determine the underlying structural and dynamical processes in solution phase reactions involving diatomic solutes. This characterization is necessary to predict solvent effects on process involving larger molecules. The impulsive photodissociation of mercuric iodide in ethanol, HgI2 → HgI + I, produces highly vibrationally excited HgI with narrow bond length distributions. This has been used as a prototype to study wavepacket motion, vibrational relaxation and rotational dynamics. The vibrational energy decay rate of HgI obtained from the EMD simulations is in quantitative agreement with the experimentally determined value. Energy dissipation is mainly facilitated by the Lennard-Jones force fluctuations. The NEMD simulations support the experimental observation of the vibrational wavepacket motion on the rotational dynamics of the HgI which strongly depends on the variations in the partial charges of HgI with internuclear distance. Another system considered in this thesis work, the aqueous hypochlorite ion, undergoes light induced charge shifting from the negatively charged O atom (ClO−) to the Cl atom (OCl−). The charge shifting event, ClO− → OCl− , is used as a prototype to study solvation dynamics. The NEMD simulations predict that solvent response occurs on two timescales which are close to those measured by experiments on the same system. The rapid and slower time components have been associated with the destruction of solvent structure around the O atom and the creation of a new structure around the Cl atom, respectively. The applicability of linear response to this process is also examined with an eye toward possible future experiments. The curvatures of the harmonic free energy surfaces of ClO− and OCl − are not the same indicating that there is nonlinearity in the solvation dynamics caused by the asymmetry of the system: The average solvent s

Published
1998

49. Binding and Movement of Individual Cel7A Cellobiohydrolases on Crystalline Cellulose Surfaces Revealed by Single-molecule Fluorescence Imaging.

Author

Jaemyeong Jung, Sethi, Anurag, Gaiotto, Tiziano, Han, Jason J., Jeoh, Tina, Gnanakaran, Sandrasegaram, and Goodwin, Peter M.

Subjects
*CELLULOSE 1,4-beta-cellobiosidase, *TRICHODERMA reesei, *BIOMASS energy research, *CATALYSIS research, *CELLULASE
Abstract

The efficient catalytic conversion of biomass to bioenergy would meet a large portion of energy requirements in the near future. A crucial step in this process is the enzyme-catalyzed hydrolysis of cellulose to glucose that is then converted into fuel such as ethanol by fermentation. Here we use single-molecule fluorescence imaging to directly monitor the movement of individual Cel7A cellobiohydrolases from Trichoderma reesei (TrCel7A) on the surface of insoluble cellulose fibrils to elucidate molecular level details of cellulase activity. The motion of multiple, individual TrCel7A cellobiohydrolases was simultaneously recorded with ~15-nm spatial resolution. Time-resolved localization microscopy provides insights on the activity of TrCel7A on cellulose and informs on nonproductive binding and diffusion. We measured single-molecule residency time distributions of TrCel7A bound to cellulose both in the presence of and absence of cellobiose the major product and a potent inhibitor of Cel7A activity. Combining these results with a kinetic model of TrCel7A binding provides microscopic insight into interactions between TrCel7A and the cellulose substrate. [ABSTRACT FROM AUTHOR]

Published
2013
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