We compare the performance of two different RNA force fields in four water models simulating conformational ensembles r(GACC) and r(CCCC). With increased sampling facilitated by multidimensional replica exchange molecular dynamics (M-REMD), populations are compared to NMR data evaluate field reliability. The combination AMBER ff12 with vdWbb modifications OPC model produces results quantitative agreement ensemble that have eluded us date.

Recent modifications and improvements to standard nucleic acid force fields have attempted fix problems issues that been observed as longer timescale simulations become routine. Although previous work has shown the ability fold UUCG stem–loop structure, until now no group quantify performance of current using highly converged structural populations tetraloop conformational ensemble. In this study, we report use multiple independent sets multidimensional replica exchange molecular dynamics...

A necessary step to properly assess and validate the performance of force fields for biomolecules is exhaustively sample accessible conformational space, which challenging large RNA structures. Given questions regarding reliability modeling structure dynamics with current methods, we have begun use tetranucleotides evaluate fields. These systems, though small, display considerable variability complete sampling standard simulation methods remains challenging. Here compare discuss known...

Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies different states a system, which in turn requires well-converged sampling ensemble possible structures. Enhanced techniques are often applied to provide faster convergence than is with traditional simulations. Hamiltonian replica exchange (H-REMD) particularly attractive method, it allows incorporation variety enhanced through modifications Hamiltonians. In...

We compare the performance of five magnesium (Mg(2+)) ion models in simulations an RNA stem loop which has experimentally determined divalent dependent conformational shift. show that despite their differences parametrization and resulting van der Waals terms, including functional form nonbonded potential, when adopts its folded conformation, all behave similarly across ten independent microsecond length with each model. However, entire structure ensemble is accounted for, chelation Mg(2+)...

Base flipping is a common strategy utilized by many enzymes to gain access the functional groups of nucleic acid bases in duplex DNA which are otherwise protected backbone and hydrogen bonding with their partner bases. Several X-ray crystallography studies have revealed flipped conformations nucleotides bound enzymes. However, little known about base-flipping process itself, even less role Computational used umbrella sampling elicit free energy profile using pseudodihedral angle represent...

The nudged elastic band method (NEB) can be used to find a minimum energy path between two given starting structures. This has been available in the standard release of Amber9 and Amber10 suite programs. In this paper novel implementation will discussed, which is applied only specific, user-defined subset atoms particular system, returning comparable results pathways as for an alanine dipeptide test system. allows incorporation explicit solvent with simulated systems, may preferred many...

Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in recognition of oxoG by Fpg its mutants a key phenylalanine residue, which intercalates next damaged base, changed either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled Fpg, as evident F110W traces, less extensively than oxoG. The...

We describe the conformational ensemble of single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist A-form-like structures variations thereof. These are not present pool generated FARFAR2. By comparing with available nuclear magnetic resonance (NMR) measurements, we show that presence both other extended is necessary to quantitatively explain experimental data. To further...

Antibody‐based pharmaceuticals are the leading biologic drug platform (> $75B/year). Despite a wealth of information collected on them, there is still lack knowledge their inter‐domain structural distributions, which impedes innovation and development. To address this measurement gap, we have developed new methodology to derive biomolecular structure ensembles from distance distribution measurements via library tagged proteins bound an unlabeled otherwise unmodified target biologic. We...

Computational predictions of biomolecular structure via artificial intelligence (AI) based approaches, as exemplified by AlphaFold software, have the potential to model all life's biomolecules. We performed oligonucleotide prediction and gauged accuracy AI-generated models their agreement with experimental solution-state observables. find parts these in good data, others falling short ground truth. The latter include internal or capping loops, noncanonical base pairings, regions involving...

Monoclonal antibodies are utilized in a wide range of biomedical applications. The NIST monoclonal antibody is resource for developing analysis methods based biopharmaceutical platforms. Techniques from topological data quantify structural features such as loops and tunnels which not easily measured by classical methods. In this paper, we introduce the Gaussian CROCKER column differences (GCCD) matrix, augments standard summaries with biological sequence information. We use GCCD matrices to...

Base eversion is a fundamental process in the biochemistry of nucleic acids, allowing proteins engaged DNA repair and epigenetic modifications to access target bases DNA. Crystal structures reveal end points these processes, but not pathways involved dynamic base recognition. To elucidate pathway taken by 8-oxoguanine during excision Fpg, we calculated free energy surfaces damaged through major minor grooves. The groove barrier (6-7 kcal/mol) are consistent with previously reported results...

8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 and H7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate remove 8-oxoG through extrusion excision. To date, it remains unclear how OGG1 efficiently distinguishes large excess of undamaged bases. We recently showed that formamidopyrimidine–DNA (Fpg), bacterial functional analog OGG1, selectively facilitate eversion oxoG stabilizing several...

In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre achieve their exquisite specificity. It is widely believed that substrate recognition by such involves a series of conformational changes enzyme–DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for mechanism limited few systems. We report discrimination between oxidative lesion,...

The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide adopts catalytically active tertiary structure includes kissing hairpin complex formed by stem-loop I and V (SLV). five-nucleotide 5'-rUGACU loop the isolated SLV adopt Mg(2+)-dependent U-turn solution NMR. is examined here molecular dynamics simulations in presence monovalent divalent ions. Simulations confirm on an all-atom level hypotheses for...

Previous reports present different models for the stabilization of Fc-FcγRI immune complex. Although accord exists on importance L235 in IgG1 and some hydrophobic contacts complex stabilization, discord regarding existence stabilizing glycoprotein between glycans a conserved FG-loop (171MGKHRY176) FcγRIa. Complexes formed from FcγRIa receptor IgG1s containing biantennary with N-acetylglucosamine, galactose, α2,6-N-acetylneuraminic terminations were measured by hydrogen-deuterium exchange...

We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference Material 8671 (NISTmAb) to enable systematic computational investigations high-concentration physical instabilities such as phase separation, clustering, and aggregation. Our coarse-graining strategy captures atomic-resolution interactions with approach that is orders magnitude more efficient than atomistic models, assuming biomolecule can be decomposed into one or rigid bodies known, fixed structures. This...

Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides aptamers can incorporate various modified to target specific biomolecules for activities. Molecular dynamics simulations accelerate design development these systems with noncanonical by observing intricate dynamic properties relative stability on all-atom level. However, modeling is...

Monoclonal antibodies (mAbs) represent an important platform for the development of biotherapeutic products. Most mAbs are produced in mammalian cells, but several made Escherichia coli, including therapeutic fragments. The NISTmAb is a well-characterized reference material widely available to facilitate both originator biologics and biosimilars. Here, when expressing from codon-optimized constructs E. coli (eNISTmAb), truncated variant its heavy chain was observed. N-terminal protein...

The interactions in the tertiary structure of a ribosomal RNA fragment GTPase Associating Center (GAC) have been experimentally studied, but roles bound and diffuse cations its folding pathway not yet fully elucidated. Melting experiments shown that temperature first two distinguishable transitions unfolding GAC can be regulated by altering magnesium concentration, physical interpretation such ion-dependent effects on clearly understood spite availability crystal structures depict many...