SanGiovanni, John Paul, Arking, Dan E., Iyengar, Sudha K., Elashoff, Michael, Clemons, Traci E., Reed, George F., ...
BACKGROUND: Age-related macular degeneration (AMD), a chronic neurodegenerative and neovascular retinal disease, is the leading cause of blindness in elderly people of western European origin. While...
Molecular Dynamics Investigations of Lipid Langmuir Monolayers Using a Coarse-Grain Model (2008)
Steve O. Nielsen, Carlos F. Lopez, Preston B. Moore, John C. Shelley, Michael L. Klein
Carlos F. Lopez, Steven O. Nielsen, Goundla Srinivas, William F. Degrado, Michael L. Klein
Abstract: Knowledge of the mechanism of action of antimicrobial agents is crucial for the development of new compounds to combat microbial pathogens. To this end, computational studies on the...
Unfolding a Linker between Helical Repeats (2008)
Vanessa Ortiz, Steven O. Nielsen, Michael L. Klein, Dennis E. Discher
Multi-domain proteins prove to be a dominant fraction of the proteome, 1 but the physical roles of linkers between domains as domain separators and/or connectors are not always clear. Multirepeat
Dissipative particle dynamics simulations of polymersomes (2008)
Vanessa Ortiz, Steven O. Nielsen, Dennis E. Discher, Michael L. Klein, Reinhard Lipowsky, Julian Shillcock
Ekta Khurana, Steven O. Nielsen, Bernd Ensing, Michael L. Klein
The self-assembly of cyclic D,L-R-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular...
Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics (2008)
Johnson, Robert R., Johnson, A. T. Charlie, Klein, Michael L.
DNA-carbon nanotube hybrids (DNA-CN) are novel nanoscale materials that consist of single-wall carbon nanotubes (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent...
De Vivo, Marco, Dal Peraro, Matteo, Klein, Michael L.
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA x DNA hybrids. This enzyme...
Vanessa Ortiz, Steven O. Nielsen, Michael L. Klein, Dennis E. Discher, Vanessa Ortiz, Steven O. Nielsen, ...
ABSTRACT: Atomistic, coarsegrain, and mesoscopic computer simulation methods applied recently to the study of block copolymer assemblies in solution are reviewed. At the atomic level, particle-based...
Gemini Surfactants at the Air/Water Interface: A Fully Atomistic Molecular Dynamics Study † (2006)
Ekta Khurana, Steven O. Nielsen, Michael L. Klein
Gemini surfactants typically consist of two single-chain surfactants chemically linked by a spacer molecule. We report herein the results of fully atomistic molecular dynamics (MD) simulations of a...
Energy Conservation in Adaptive Hybrid Atomistic/ Coarse-Grain Molecular Dynamics (2006)
Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, Michele Parrinello
Abstract: Multiscale computer simulation algorithms are required to describe complex molecular systems with events occurring over a range of time and length scales. True multiscale simulations must...
Blumberger, Jochen, Tavernelli, Ivano, Klein, Michael L., Sprik, Michiel
Redox potentials measure the free energy required to transfer a mol. species (ion) between two states of different total charge. In soln. a major contribution to the redox potential is the hydration...
Steve O. Nielsen, Bernd Ensing, Vanessa Ortiz, Michael L. Klein
ABSTRACT The perturbations induced in a lipid bilayer by the presence of a transmembrane nanotube are investigated using coarse grained molecular dynamics. Meniscus formation by the lipids and...
Structure and Dynamics of Model Pore Insertion into a Membrane (2005)
Carlos F. Lopez, Steve O. Nielsen, Bernd Ensing, Preston B. Moore, Michael L. Klein
ABSTRACT A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a...
Meta-analysis of genome scans of age-related macular degeneration (2005)
Fisher, Sheila A., Abecasis, Goncalo R., Yashar, Beverly M., Zareparsi, Sepideh, Swaroop, Anand, Iyengar, Sudha K., ...
A genetic contribution to the development of age-related macular degeneration (AMD) is well established. Several genome-wide linkage studies have identified a number of putative susceptibility loci...
Meta-Analysis of Genome Scans of Age-Related Macular Degeneration (2005)
Fisher, Sheila A, Abecasis, Goncalo R, Yashar, Beverly M, Zareparsi, Sepideh, Swaroop, Anand, Iyengar, Sudha K, ...
A genetic contribution to the development of age-related macular degeneration (AMD) is well established. Several genome-wide linkage studies have identified a number of putative susceptibility loci...
Steve O Nielsen, Carlos F Lopez, Goundla Srinivas, Michael L Klein
Coarse grain models and the computer simulation of
Steve O. Nielsen, Carlos F. Lopez, Ivaylo Ivanov, Preston B. Moore, Michael L. Klein
ABSTRACT Molecular dynamics results are presented for a coarse-grain model of 1,2-di-n-alkanoyl-sn-glycero-3phosphocholine, water, and a capped cylindrical model of a transmembrane peptide. We first...
Magistrato, Alessandra, DeGrado, William F., Laio, Alessandro, Rothlisberger, Ursula, VandeVondele, Joost, Klein, Michael L.
The structural and dynamical properties of the four a-helix bundle Due Ferri 1, which is a generic mimic of diiron proteins, have been explored using d. functional theory (DFT) based and hybrid...
Revolutionizing Science and Engineering Through Cyberinfrastructure (2003)
Daniel E. Atkins, Kelvin K. Droegemeier, Stuart I. Feldman, Hector Garcia-molina, Michael L. Klein, David G. Messerschmitt, ...
This report was prepared by an officially appointed advisory panel to the National Science Foundation, however, any opinions, findings, and conclusions or recommendations expressed in this material...
Simulation of Diblock Copolymer Self-Assembly, Using a Coarse-Grain Model (2003)
Goundla Srinivas, John C. Shelley, Steve O. Nielsen, Dennis E. Discher, Michael L. Klein
A coarse-grain model for amphiphilic diblock copolymers is developed by fitting the required parameters to properties taken from all-atom molecular dynamics simulations and experimental data....
Revolutionizing Science and Engineering Through Cyberinfrastructure (2003)
Daniel E. Atkins, Kelvin K. Droegemeier, Stuart I. Feldman, Hector Garcia-molina, Michael L. Klein, David G. Messerschmitt, ...
This report was prepared by an officially appointed advisory panel to the National Science Foundation, however, any opinions, findings, and conclusions or recommendations expressed in this material...
Schultz, Dennis W., Klein, Michael L., Humpert, Andrea J., Luzier, Christina W., Persun, Vesna, Schain, Mitchell, ...
Age-related macular degeneration (AMD) is a common cause of severe vision loss. Identification of the genes involved in AMD will lead to a better understanding of this disease at the molecular level,...
Schultz, Dennis W., Klein, Michael L., Humpert, Andrea J., Luzier, Christina W., Persun, Vesna, Schain, Mitchell, ...
Age-related macular degeneration (AMD) is a common cause of severe vision loss. Identification of the genes involved in AMD will lead to a better understanding of this disease at the molecular level,...
Schultz, Dennis W., Klein, Michael L., Humpert, Andrea J., Luzier, Christina W., Persun, Vesna, Schain, Mitchell, ...
Age-related macular degeneration (AMD) is a common cause of severe vision loss. Identification of the genes involved in AMD will lead to a better understanding of this disease at the molecular level,...
Magistrato, Alessandra, Rothlisberger, Ursula, Klein, Michael L.
A biomimetic four-helix bundle with a binuclear active site (DF1), bearing Zn, Mn or Fe as transition metals, has been synthesized and characterized. The carboxylate bridged binuclear motif of DF1...
Magistrato, Alessandra, Rothlisberger, Ursula, Klein, Michael L.
A biomimetic four-helix bundle with a binuclear active site (DF1), bearing Zn, Mn or Fe as transition metals, has been synthesized and characterized. The carboxylate bridged binuclear motif of DF1...
Evolution of Fragments Formed at the Rupture of a Knotted Alkane Molecule (1999)
Saitta, A. Marco, Klein, Michael L.
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles...
Saitta, A. Marco, Klein, Michael L.
The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics...
Influence of a knot on the strength of a polymer strand (1999)
Saitta, A. Marco, Soper, Paul D., Wasserman, E., Klein, Michael L.
Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance'...
Conformational and orientational order and disorder in solid polytetrafluoroethylene (1999)
Sprik, Michiel, Rothlisberger, Ursula, Klein, Michael L.
The low-pressure phase diagram of solid poly(tetrafluoroethylene) (PTFE/Teflon) has been investigated using const.-temp./const.-pressure mol.-dynamics techniques and a new all-atom potential model...
Rothlisberger, Ursula, Sprik, Michiel, Klein, Michael L.
The polymn. of isoprene induced by alkyl lithium compds. in hydrocarbon solvents is known to proceed with a high stereoselectivity to (Z)-1,4-polyisoprene. We have studied the initiation step of this...
Molecular dynamics simulation of a synthetic ion channel (1998)
Qingfeng Zhong, Qing Jiang, Preston B. Moore, Dennis M. Newns, Michael L. Klein
ABSTRACT A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four �-helical peptides, each of which is composed of the amino acids leucine...
Sprik, Michiel, Roethlisberger, Ursula, Klein, Michael L.
The nature of the orientational, translational, and conformational disorder exhibited by poly(tetrafluoroethylene) has been characterized with the help of mol. dynamics calcns. based on a new...
The torsional potential of perfluoro n-alkanes: a density functional study (1996)
Rothlisberger, Ursula, Laasonen, Kari, Klein, Michael L., Sprik, Michiel
The structural, vibrational, and conformational properties of small perfluoro n-alkanes CnF2n (n ? 5) have been studied with different d. functional models. The relative conformational energies are...
Roethlisberger, Ursula, Klein, Michael L.
The structural, electronic, and dynamic properties of the organolithium compd. C2H2Li2 were studied via ab initio mol. dynamics simulations based on the Car-Parrinello method. Dynamic simulated...
Simulation of self-assembled monolayers:microscopic structure of amino alkylthiols (1994)
Rothlisberger, Ursula, Klein, Michael L., Sprik, Michiel
We present the results of mol. dynamics calcns. carried out on self-assembled monolayers (SAMs) formed from alkyl thiols chemisorbed on a gold (111) substrate. The alkyl tails are functionalized by...
Roethlisberger, Ursula, Klein, Michael L.
The torsional potential about the central C-C bond in n-butane was investigated as a test case to probe the capability of d. functional methods for the description of weak interaction potentials....
Rothlisberger, Ursula, Klein, Michael L., Sprik, Michiel
The structure of self-assembled monolayers of a long-chain perfluoro mercaptan was studied by using mol. dynamics simulations. The particular system studied (e.g., perfluorooctyl mercaptoethylamide)...
High-density structures and phase transition in an ionic model of H2O ice (1989)
Demontis, Pierfranco, Klein, Michael L., LeSar, Richard
A self-consistent ionic model of water (protons and O2- ions) has been used to explore the low-temperature, high-pressure properties of ice. Interionic interactions were calculated with the...
New high-pressure phases of ice (1988)
Demontis, Pierfranco, LeSar, Richard, Klein, Michael L.
An ionic model has been used in conjunction with classical constant-pressure molecular-dynamics calculations to explore the properties of possible high-pressure phases of ice. Around 100 GPa, the...
Microfilm.
De novo design of biomimetic antimicrobial polymers
Tew, Gregory N., Liu, Dahui, Chen, Bin, Doerksen, Robert J., Kaplan, Justin, Carroll, Patrick J., ...
The design of polymers and oligomers that mimic the complex structures and remarkable biological properties of proteins is an important endeavor with both fundamental and practical implications....
Understanding nature's design for a nanosyringe
Lopez, Carlos F., Nielsen, Steve O., Moore, Preston B., Klein, Michael L.
Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion...
Ensing, Bernd, Klein, Michael L.
Recently, we computed the 3D free energy surface of the base-induced elimination reaction between F– and CH3CH2F by using a powerful technique within Car–Parrinello molecular dynamics simulation....
Lopez, Carlos F, Montal, Mauricio, Blasie, J Kent, Klein, Michael L, Moore, Preston B
Molecular dynamics (MD) simulations have been carried out on bundles of the channel-forming transmembrane (TM) domain of the viral protein U (VPU(1-27) and VPU(6-27)) from the human immunodeficiency...
Nielsen, Steve O., Lopez, Carlos F., Ivanov, Ivaylo, Moore, Preston B., Shelley, John C., Klein, Michael L.
Molecular dynamics results are presented for a coarse-grain model of 1,2-di-n-alkanoyl-sn-glycero-3-phosphocholine, water, and a capped cylindrical model of a transmembrane peptide. We first...
Saiz, Leonor, Klein, Michael L.
We have studied the structure and properties of a bundle of α-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle...
Pickholz, Mónica, Saiz, Leonor, Klein, Michael L.
To gain insights into the molecular level mechanism of drug action at the membrane site, we have carried out extensive molecular dynamics simulations of a model membrane in the presence of a volatile...
Structure and Dynamics of Model Pore Insertion into a Membrane
Lopez, Carlos F., Nielsen, Steve O., Ensing, Bernd, Moore, Preston B., Klein, Michael L.
A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a transmembrane...
Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study
Nielsen, Steve O., Ensing, Bernd, Ortiz, Vanessa, Moore, Preston B., Klein, Michael L.
The perturbations induced in a lipid bilayer by the presence of a transmembrane nanotube are investigated using coarse grained molecular dynamics. Meniscus formation by the lipids and tilting of the...
De novo design of biomimetic antimicrobial polymers
Tew, Gregory N., Liu, Dahui, Chen, Bin, Doerksen, Robert J., Kaplan, Justin, Carroll, Patrick J., ...
The design of polymers and oligomers that mimic the complex structures and remarkable biological properties of proteins is an important endeavor with both fundamental and practical implications....
Understanding nature's design for a nanosyringe
Lopez, Carlos F., Nielsen, Steve O., Moore, Preston B., Klein, Michael L.
Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion...
Ensing, Bernd, Klein, Michael L.
Recently, we computed the 3D free energy surface of the base-induced elimination reaction between F– and CH3CH2F by using a powerful technique within Car–Parrinello molecular dynamics simulation....
Age-Related Macular Degeneration—a Genome Scan in Extended Families
Majewski, Jacek, Schultz, Dennis W., Weleber, Richard G., Schain, Mitchell B., Edwards, Albert O., Matise, Tara C., ...
We performed a genomewide scan and genetic linkage analysis, to identify loci associated with age-related macular degeneration (AMD). We collected 70 families, ranging from small nuclear families to...
Lopez, Carlos F, Montal, Mauricio, Blasie, J Kent, Klein, Michael L, Moore, Preston B
Molecular dynamics (MD) simulations have been carried out on bundles of the channel-forming transmembrane (TM) domain of the viral protein U (VPU(1-27) and VPU(6-27)) from the human immunodeficiency...
Nielsen, Steve O., Lopez, Carlos F., Ivanov, Ivaylo, Moore, Preston B., Shelley, John C., Klein, Michael L.
Molecular dynamics results are presented for a coarse-grain model of 1,2-di-n-alkanoyl-sn-glycero-3-phosphocholine, water, and a capped cylindrical model of a transmembrane peptide. We first...
Saiz, Leonor, Klein, Michael L.
We have studied the structure and properties of a bundle of α-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle...
Pickholz, Mónica, Saiz, Leonor, Klein, Michael L.
To gain insights into the molecular level mechanism of drug action at the membrane site, we have carried out extensive molecular dynamics simulations of a model membrane in the presence of a volatile...
Structure and Dynamics of Model Pore Insertion into a Membrane
Lopez, Carlos F., Nielsen, Steve O., Ensing, Bernd, Moore, Preston B., Klein, Michael L.
A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a transmembrane...
Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study
Nielsen, Steve O., Ensing, Bernd, Ortiz, Vanessa, Moore, Preston B., Klein, Michael L.
The perturbations induced in a lipid bilayer by the presence of a transmembrane nanotube are investigated using coarse grained molecular dynamics. Meniscus formation by the lipids and tilting of the...
Role of Aromatic Localization in the Gating Process of a Potassium Channel
Domene, Carmen, Vemparala, Satyavani, Klein, Michael L., Vénien-Bryan, Catherine, Doyle, Declan A.
Position of the transmembrane aromatic residues of the KirBac1.1 potassium channel shifts from an even distribution in the closed state toward the membrane/solute interface in the open state model....
Vemparala, Satyavani, Saiz, Leonor, Eckenhoff, Roderic G., Klein, Michael L.
Molecular dynamics simulations have been performed to investigate the partitioning of the volatile anesthetic halothane from an aqueous phase into a coexisting hydrated bilayer, composed of...
Francis, Peter J., Schultz, Dennis W., Hamon, Sara, Ott, Jurg, Weleber, Richard G., Klein, Michael L.
A Stable Water Chain in the Hydrophobic Pore of the AmtB Ammonium Transporter
Lamoureux, Guillaume, Klein, Michael L., Bernèche, Simon
The accessibility of water molecules to the pore of the AmtB ammonium transporter is studied using molecular dynamics simulations. Free energy calculations show that the so-called hydrophobic pore...
Embedded cholesterol in the nicotinic acetylcholine receptor
Brannigan, Grace, Hénin, Jérôme, Law, Richard, Eckenhoff, Roderic, Klein, Michael L.
The nicotinic acetylcholine receptor (nAChR) is a cation-selective channel central to both neuronal and muscular processes and is considered the prototype for ligand-gated ion channels, motivating a...
SanGiovanni, John Paul, Arking, Dan E., Iyengar, Sudha K., Elashoff, Michael, Clemons, Traci E., Reed, George F., ...
Vemparala, Satyavani, Domene, Carmen, Klein, Michael L.
A variety of experiments suggest that membrane proteins are important targets of anesthetic molecules, and that ion channels interact differently with anesthetics in their open and closed...
Khurana, Ekta, Peraro, Matteo Dal, DeVane, Russell, Vemparala, Satyavani, DeGrado, William F., Klein, Michael L.
The M2 protein of the influenza A virus is activated by low endosomal pH and performs the essential function of proton transfer into the viral interior. The resulting decrease in pH within the virion...
Identification of a fluorescent general anesthetic, 1-aminoanthracene
Butts, Christopher A., Xi, Jin, Brannigan, Grace, Saad, Abdalla A., Venkatachalan, Srinivasan P., Pearce, Robert A., ...
We identified a fluorophore, 1-aminoanthracene (1-AMA), that is anesthetic, potentiates GABAergic transmission, and gives an appropriate dissociation constant, Kd ≈ 0.1 mM, for binding to the...