Search results for: David A. Case

Items from 1 to 20 out of 119 results

article

Enhanced TROSY Effect in [2‐¹⁹F, 2‐¹³C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution

Fabian Juen, David Glänzer, Raphael Plangger, Valentina Kugler, more

Angewandte Chemie International Edition > 63 > 9 > n/a - n/a

Large RNAs are central to cellular functions, but characterizing such RNAs remains challenging by solution NMR. We present two labeling technologies based on [2‐¹⁹F, 2‐¹³C]‐adenosine, which allow the incorporation of aromatic ¹⁹F‐¹³C spin pairs. The labels when coupled with the transverse relaxation optimized spectroscopy (TROSY) enable us to probe RNAs comprising up to 124 nucleotides. With our new...

article

Enhanced TROSY Effect in [2‐¹⁹F, 2‐¹³C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution

Fabian Juen, David Glänzer, Raphael Plangger, Valentina Kugler, more

Angewandte Chemie > 136 > 9 > n/a - n/a

article

New experimental evidence for pervasive dynamics in proteins

Erik R.P. Zuiderweg, David A. Case

Protein Science > 32 > 5 > n/a - n/a

There is ample computational, but only sparse experimental data suggesting that pico‐ns motions with 1 Å amplitude are pervasive in proteins in solution. Such motions, if present in reality, must deeply affect protein function and protein entropy. Several NMR relaxation experiments have provided insights into motions of proteins in solution, but they primarily report on azimuthal angle variations...

article

Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain

Jonathan K. Williams, Baifan Wang, Andrew Sam, Cody L. Hoop, more

Proteins: Structure, Function, and Bioinformatics > 90 > 5 > 1044 - 1053

Since the identification of the SARS‐CoV‐2 virus as the causative agent of the current COVID‐19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor‐binding domain (RBD) and the human angiotensin converting enzyme 2 (ACE2) receptor. This has provided a detailed picture of the end point structure of the RBD‐ACE2 binding event, but what remains...

article

Molecular dynamics simulations of macromolecular crystals

David S. Cerutti, David A. Case

Wiley Interdisciplinary Reviews: Computational Molecular Science > 9 > 4 > n/a - n/a

The structures of biological macromolecules would not be known to their present extent without X‐ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the...

article

Interview with David A. Case: On force fields, biomolecular modeling, and NMR

David A. Case, Nikolai R. Skrynnikov

Concepts in Magnetic Resonance Part A > 45A > 5 > n/a - n/a

Prof. David Case is based in the Department of Chemistry and Chemical Biology at Rutgers University. In this interview he speaks about force field development and validation, predictive power of MD models, combining physics‐based force fields with empirical scoring functions, MD modeling of disordered proteins and RNA, synergies between MD simulations and NMR measurements, and chemical shift calculations...

article

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

Honglue Shi, Mary C. Clay, Atul Rangadurai, Bharathwaj Sathyamoorthy, more

Journal of Biomolecular NMR > 2018 > 70 > 4 > 229-244

NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson–Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m¹A) and guanine (m¹G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m¹A–T Hoogsteen bps reveal significant...

article

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, more

Journal of Computer-Aided Molecular Design > 2017 > 31 > 8 > 777-777

article

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, more

Journal of Computer-Aided Molecular Design > 2017 > 31 > 1 > 147-161

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared...

article

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Paul D. Adams, Kathleen Aertgeerts, Cary Bauer, Jeffrey A. Bell, more

Structure > 2016 > 24 > 4 > 502-508

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least...

article

Virtual substitution scan via single‐step free energy perturbation

Ying‐Chih Chiang, Yi Wang, David A. Case

Biopolymers > 105 > 6 > 324 - 336

With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the “recycling” of these trajectories,...

article

Modeling bond correlations in denatured proteins and polypeptides

Marcos R. Betancourt, David A. Case

Biopolymers > 105 > 6 > 312 - 323

Bond‐orientational correlations for finite‐length homopolypeptides and a selected group of denatured proteins are obtained by numerical simulations using a polypeptide model with a potential of mean force. These correlations characterize the stiffness of the polypeptide backbone and are generally described by either an exponential or a power‐law decay in the asymptotic limit. However, for finite length...

article

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, more

Journal of Computer-Aided Molecular Design > 2016 > 30 > 7 > 533-539

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck–Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI...

article

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

Pawel A. Janowski, Chunmei Liu, Jason Deckman, David A. Case

Protein Science > 25 > 1 > 87 - 102

Molecular dynamics simulations of crystals can enlighten interpretation of experimental X‐ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg‐white...

article

All-atom crystal simulations of DNA and RNA duplexes

Chunmei Liu, Pawel A. Janowski, David A. Case

Biochimica et Biophysica Acta (BBA) - General Subjects > 2015 > 1850 > 5 > 1059-1071

Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data.We report simulations of DNA and RNA duplexes in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2],...

article

DOCK 6: Impact of new features and current docking performance

William J. Allen, Trent E. Balius, Sudipto Mukherjee, Scott R. Brozell, more

Journal of Computational Chemistry > 36 > 15 > 1132 - 1156

This manuscript presents the latest algorithmic and methodological developments to the structure‐based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry‐corrected root‐mean‐square deviation algorithm, a database filter, and docking forensic tools. An important strategy...

article

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Jason Swails, Tong Zhu, Xiao He, David A. Case

Journal of Biomolecular NMR > 2015 > 63 > 2 > 125-139

We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement...

article

Effect O6‐guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations

Mahmut Kara, Tomas Drsata, Filip Lankas, Martin Zacharias, more

Biopolymers > 103 > 1 > 23 - 32

Alkylation of guanine at the O6 atom is a highly mutagenic DNA lesion because it alters the coding specificity of the base causing G:C to A:T transversion mutations. Specific DNA repair enzymes, e.g. O⁶‐alkylguanin‐DNA‐Transferases (AGT), recognize and repair such damage after looping out the damaged base to transfer it into the enzyme active site. The exact mechanism how the repair enzyme identifies...

article

Binding free energy calculations between bovine β‐lactoglobulin and four fatty acids using the MMGBSA method

Martiniano Bello, David A. Case

Biopolymers > 101 > 10 > 1010 - 1018

The bovine dairy protein β‐lactoglobulin (βlg) is a promiscuous protein that has the ability to bind several hydrophobic ligands. In this study, based on known experimental data, the dynamic interaction mechanism between bovine βlg and four fatty acids was investigated by a protocol combining molecular dynamics (MD) simulations and molecular mechanics generalized Born surface area (MMGBSA) binding...

article

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

Indrajit Deb, Joanna Sarzynska, Lennart Nilsson, Ansuman Lahiri, more

Biopolymers > 101 > 10 > 985 - 991

The structural effects of the commonly occurring modified nucleoside dihydrouridine (D) observed experimentally in model oligonucleotides include a strong destabilization of the C3′‐endo sugar conformation of D, the disruption of stacking interactions of neighboring residues with D and a possible destabilization of the C3′‐endo sugar pucker of the 5′‐neighboring nucleoside. Our simulations with a...

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INFONA - science communication portal

Search results for: David A. Case

Enhanced TROSY Effect in [2‐¹⁹F, 2‐¹³C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution

Enhanced TROSY Effect in [2‐¹⁹F, 2‐¹³C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution

New experimental evidence for pervasive dynamics in proteins

Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain

Molecular dynamics simulations of macromolecular crystals

Interview with David A. Case: On force fields, biomolecular modeling, and NMR

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Virtual substitution scan via single‐step free energy perturbation

Modeling bond correlations in denatured proteins and polypeptides

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

All-atom crystal simulations of DNA and RNA duplexes

DOCK 6: Impact of new features and current docking performance

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Effect O6‐guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations

Binding free energy calculations between bovine β‐lactoglobulin and four fatty acids using the MMGBSA method

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations

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