Structure Of Biomolecules Research Articles

When molecules come to life – Using Augmented reality for studying protein structure in Cell Biology class

Most Undergraduate Biology courses cover an incredibly large range of topics integrating complex information at molecular, cellular, genetic and at the organismal level. Translating concepts from one level of thought to another and crossing disciplines equally and fluidly largely depends on how well students understand the structure‐function relationship at the micro and macro level. A survey of the literature shows that despite having encountered these structures of biomolecules in their earlier courses, students lack an ability to visualize molecules and interactions. Most classroom curriculums use textbooks and lecture slides with straightforward two‐dimensional structures that make it hard for students to visualize these macromolecules. To improve motivation and to promote student interactivity, in Cell Biology classes I have used molecular models in Augmented reality to reform content delivery by using interactive active learning techniques. This presentation will discuss ways for instructors to implement Augmented reality in their classes to help students better understand concepts of structure and function of Biomolecules.

On the fly swapping algorithm for ordering of degrees of freedom in density matrix renormalization group

Density matrix renormalization group (DMRG) and its time-dependent variants have found widespread applications in quantum chemistry, including ab initio electronic structure of complex bio-molecules, spectroscopy for molecular aggregates, and charge transport in bulk organic semiconductors. The underlying wavefunction ansatz for DMRG, matrix product state (MPS), requires mapping degrees of freedom (DOF) into a one-dimensional topology. DOF ordering becomes a crucial factor for DMRG accuracy. In this work, we propose swapping neighboring DOFs during the DMRG sweeps for DOF ordering, which we term ‘on the fly swapping’ (OFS) algorithm. We show that OFS is universal for both static and time-dependent DMRG with minimum computational overhead. Examples are given for one dimensional antiferromagnetic Heisenberg model, ab initio electronic structure of N2 molecule, and the S1/S2 internal conversion dynamics of pyrazine molecule. It is found that OFS can indeed improve accuracy by finding better DOF ordering in all cases.

A multi-million image Serial Femtosecond Crystallography dataset collected at the European XFEL

Serial femtosecond crystallography is a rapidly developing method for determining the structure of biomolecules for samples which have proven challenging with conventional X-ray crystallography, such as for membrane proteins and microcrystals, or for time-resolved studies. The European XFEL, the first high repetition rate hard X-ray free electron laser, provides the ability to record diffraction data at more than an order of magnitude faster than previously achievable, putting increased demand on sample delivery and data processing. This work describes a publicly available serial femtosecond crystallography dataset collected at the SPB/SFX instrument at the European XFEL. This dataset contains information suitable for algorithmic development for detector calibration, image classification and structure determination, as well as testing and training for future users of the European XFEL and other XFELs.

Enhancement of the Water Affinity of Histidine by Zinc and Copper Ions.

Histidine (His) is widely involved in the structure and function of biomolecules. Transition-metal ions, such as Zn2+ and Cu2+, widely exist in biological environments, and they are crucial to many life-sustaining physiological processes. Herein, by employing density function calculations, we theoretically show that the water affinity of His can be enhanced by the strong cation–π interaction between His and Zn2+ and Cu2+. Further, the solubility of His is experimentally demonstrated to be greatly enhanced in ZnCl2 and CuCl2 solutions. The existence of cation–π interaction is demonstrated by fluorescence, ultraviolet (UV) spectroscopy and nuclear magnetic resonance (NMR) experiments. These findings are of great importance for the bioavailability of aromatic drugs and provide new insight for understanding the physiological functions of transition metal ions.

Electrostatic free energies carry structural information on nucleic acid molecules in solution.

Over the last several decades, a range of experimental techniques from x-ray crystallography and atomic force microscopy to nuclear magnetic resonance and small angle x-ray scattering have probed nucleic acid structure and conformation with high resolution both in the condensed state and in solution. We present a computational study that examines the prospect of using electrostatic free energy measurements to detect 3D conformational properties of nucleic acid molecules in solution. As an example, we consider the conformational difference between A- and B-form double helices whose structures differ in the values of two key parameters-the helical radius and rise per basepair. Mapping the double helix onto a smooth charged cylinder reveals that electrostatic free energies for molecular helices can, indeed, be described by two parameters: the axial charge spacing and the radius of a corresponding equivalent cylinder. We show that electrostatic free energies are also sensitive to the local structure of the molecular interface with the surrounding electrolyte. A free energy measurement accuracy of 1%, achievable using the escape time electrometry (ETe) technique, could be expected to offer a measurement precision on the radius of the double helix of approximately 1 Å. Electrostatic free energy measurements may, therefore, not only provide information on the structure and conformation of biomolecules but could also shed light on the interfacial hydration layer and the size and arrangement of counterions at the molecular interface in solution.

A DFT study of vibrational spectra of 5-chlorouracil with molecular structure, HOMO-LUMO, MEPs/ESPs and thermodynamic properties.

The density functional theory calculation has been carried out for the analysis of 5-chlorouracil using DFT/Gaussian 09 with GAR2PED. Recorded experimental spectra for Raman and IR of 5-chlorouracil have been analyzed all fundamental vibrational modes using the outcome results of DFT at 6-311++G** of Gaussian 09 calculations and the GaussView 5.09. To help the analysis of vibrational modes, GAR2PED program has been used in the calculation of PEDs. The charge transfer properties of 5-chlorouracil have been analyzed using HOMO and LUMO level energy analysis. HOMO and LUMO energy gap study supports the charge transfer possibility in molecule. These have been made to study for reactivity and stability of heterocyclic molecules for the analysis of antiviral drugs against the new corona virus: COVID-19. Here, the smaller energy gap of 5-chlorouracil is more responsible for charge transfer interaction in the heterocyclic drug molecules and a reason of more bioactivity. The electron density mapping within molecular electrostatic potential plot and electrostatic potential plotting within iso-surface plot have been evaluated the charge distribution concept in the molecule as the nucleophilic reactions and electrophilic sites. These computations have been used to produce the molecular charges, structure and thermodynamic functions of biomolecule. This study has been made to all internal modes of chloro group substituent at pyrimidine ring of C5 atom. The splitting of frequencies has arisen in the two species for the normal distribution modes.Graphical abstract

Adding hydrogen atoms to molecular models via fragment superimposition

BackgroundMost experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds.ResultsWe present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used.ConclusionsWe bundled the algorithm into the open-source Python package and command line program Hydride. Since usually no additional parametrization is necessary for the problem at hand, the software works out-of-box for a wide range of molecular systems usually within a few seconds of computation time. Hence, we believe that Hydride could be a valuable tool for structural biologists and biophysicists alike.

Performance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon Source.

Recent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS-WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV-Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS-WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005-2.0 Å-1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.

CD Spectroscopy to Study DNA-Protein Interactions.

Circular dichroism (CD) spectroscopy is a simple and convenient method to investigate the secondary structure and interactions of biomolecules. Recent advancements in CD spectroscopy have enabled the study of DNA-protein interactions and conformational dynamics of DNA in different microenvironments in detail for a better understanding of transcriptional regulation in vivo. The area around a potential transcription zone needs to be unwound for transcription to occur. This is a complex process requiring the coordination of histone modifications, binding of the transcription factor to DNA, and other chromatin remodeling activities. Using CD spectroscopy, it is possible to study conformational changes in the promoter region caused by regulatory proteins, such as ATP-dependent chromatin remodelers, to promote transcription. The conformational changes occurring in the protein can also be monitored. In addition, queries regarding the affinity of the protein towards its target DNA and sequence specificity can be addressed by incorporating mutations in the target DNA. In short, the unique understanding of this sensitive and inexpensive method can predict changes in chromatin dynamics, thereby improving the understanding of transcriptional regulation.

Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking

The dynamic properties of protein molecules are involved in the relationship between their structure and function. Time-resolved X-ray observation enables capturing the structures of biomolecules with picometre-scale precision. However, this technique has yet to be implemented in living animals. Here, we examined diffracted X-ray blinking (DXB) and diffracted X-ray tracking (DXT) to observe the dynamics of a protein located on intestinal cells in adult Caenorhabditis elegans. This in vivo tissue-specific DXB was examined at temperatures from 20 °C to −10 °C for a recombinant ice-binding protein from Antarctomyces psychrotrophicus (AnpIBP) connected with the cells through a transmembrane CD4 protein equipped with a glycine-serine linker. AnpIBP inhibits ice growth at subzero temperatures by binding to ice crystals. We found that the rotational motion of AnpIBP decreases at −10 °C. In contrast, the motion of the AnpIBP mutant, which has a defective ice-binding ability, did not decrease at −10 °C. The twisting and tilting motional speeds of AnpIBPs measured above 5 °C by DXT were always higher than those of the defective AnpIBP mutant. These results suggest that wild-type AnpIBP is highly mobile in solution, and it is halted at subzero temperatures through ice binding. DXB and DXT allow for exploring protein behaviour in live animals with subnano resolution precision.

Deep learning-based local quality estimation for protein structure models from cryo-EM maps

In the recent decade, an increasing number of cryo-electron microscopy (cryo-EM) maps were determined to model the tertiary structures of biomolecules. Although the resolution of determined cryo-EM maps is improving in general, there are still many cases where amino acids of a protein were assigned to the map with different confidence levels, including those with relatively high ambiguity. A common error, particularly when side-chain density is not well defined and there are poorly ordered loops between secondary structures, is for the sequence of the model to become out of register.

Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy

Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological macromolecules can be revealed by 23Na diffusion nuclear magnetic resonance (NMR) spectroscopy. NMR probe hardware capable of generating strong magnetic field gradients enables 23Na NMR-based diffusion measurements for Na+ ions in solutions of biological macromolecules and their complexes. The dynamic properties of Na+ ions interacting with the macromolecules can be investigated using apparent 23Na diffusion coefficients measured under various conditions. Our diffusion data clearly show that Na+ ions retain high mobility within the ion atmosphere around DNA. The 23Na diffusion NMR method also permits direct observation of the release of Na+ ions from nucleic acids upon protein–nucleic acid association. The entropy change due to the ion release can be estimated from the diffusion data.

Perfluorooctanoic acid (PFOA)-induced alterations of biomolecules in the wetland plant Alismaorientale

Perfluoroalkyl substances (PFASs) have been widely studied by researchers due to their environmental persistence, chemical stability and potential toxicity. Some researchers have reported the physiological and biochemical toxicity of PFASs on plants through traditional and innovative methods; however, the changes in biological macromolecules caused by PFASs are rarely studied. Here, Fourier transform infrared spectroscopy (FTIR) was used to study how exposure to perfluorooctanoic acid (PFOA) alters the structure and function of biomolecules of the wetland plant Alisma orientale. Biomass results showed that PFOA had negative effects on plant growth. FTIR results showed that PFOA could result in changes in the structures, compositions, and functions of lipids, proteins and DNA in plant cells. In the treatment groups, the ratios of CH3 to lipids and carbonyl esters to lipids increased compared with the control, while the ratios of CH2 to lipids and olefinicCH to lipids decreased, which indicated lipid peroxidation caused by PFOA exposure. Changes in the compositions and secondary structures of proteins were also found, which were indicated by the decreased ratio of amide I to amide II and the increased ratio of β-sheet to α-helix in the treatment groups compared to the control. Moreover, PFOA affected the composition of DNA by promoting the B- to A-DNA transition. These results showed that the mechanism of PFOA toxicity toward plants at the biochemical level could be illustrated by FTIR.

Mechanistic Understanding of DNA Denaturation in Nanoscale Thermal Gradients Created by Femtosecond Excitation of Gold Nanoparticles

There is significant interest in developing photothermal systems that can precisely control the structure and function of biomolecules through local temperature modulation. One specific application is the denaturation of double-stranded (ds) DNA through femtosecond (fs) laser pulse optical heating of gold nanoparticles (AuNPs); however, the mechanism of DNA melting in these systems is not fully understood. Here, we utilize 55 nm AuNPs with surface-tethered dsDNA, which are locally heated using fs laser pulses to induce DNA melting. By varying the dsDNA distance from the AuNP surface and the laser pulse energy fluence, this system is used to study how the nanosecond duration temperature increase and the steep temperature gradient around the AuNP affect dsDNA dehybridization. Through modifying the distance between the dsDNA and AuNP surface by 3.8 nm in total and the pulse energy fluence from 7.1 to 14.1 J/m2, the dehybridization rates ranged from 0.002 to 0.05 DNA per pulse, and the total amount of DNA released into solution was controlled over a range of 26-93% in only 100 s of irradiation. By shifting the dsDNA position as little as ∼1.1 nm, the average dsDNA dehybridization rate is altered up to 30 ± 2%, providing a high level of control over DNA melting and release. By comparing the theoretical temperature around the dsDNA to the experimentally derived temperature, we find that maximum or peak temperatures have a greater influence on the dehybridization rate when the dsDNA is closer to the AuNP surface and when lower laser pulse fluences are used. Furthermore, molecular dynamics simulations mimicking the photothermal heat pulse around a AuNP provide mechanistic insight into the stochastic nature of dehybridization and demonstrate increased base pair separation near the AuNP surface during laser pulse heating when compared to steady-state heating. Understanding how biological materials respond to the short-lived and non-uniform temperature increases innate to fs laser pulse optical heating of AuNPs is critical to improving the functionality and precision of this technique so that it may be implemented into more complex biological systems.

A geometry based approach to compare five metal binding sites on biomolecular structures

Characterisation of type or function of a coordination site on the structure of biomolecules - protein, DNA and RNA is a very critical task. Sometimes it is needed to compare a new site with an existing one, to predict structural properties or function of the new site and to compute various coordination statistics. Now, different coordination sites possess different geometries. So, the task is to compare an unknown site with a known one possessing the same geometries and to compute statistics regarding structural deviations. For the same purpose, in this study, three novel algorithms have been proposed that use a geometry-based concept to compare five pairs of coordination sites. To produce minimum mean square error (MSE) due to the structural deviations, some mathematical transformations have been applied on each pair of structures to make them structurally compatible. Bio-researchers get benefitted from the numerous statistical reports obtained with these algorithms.

PELDOR Measurements on Nitroxide-Labeled Oligonucleotides.

In the past decades, pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) has emerged as a powerful tool in biophysical chemistry to study the structure, dynamics, and function of biomolecules like oligonucleotides and proteins. Structural information is obtained from PDS methods in form of a distribution of distances between spin centers. Such spin centers can either be intrinsically present paramagnetic metal ions and organic radicals or may be attached to the biomolecule by means of site-directed spin labeling. The most common PDS experiment for probing interspin distances in the nanometer range is pulsed electron-electron double resonance (PELDOR or DEER). In the protocol presented here, we provide a step-by-step workflow on how to set up a PELDOR experiment on a commercially available pulsed EPR spectrometer, outline the data analysis, and highlight potential pitfalls. We suggest PELDOR measurements on nitroxide-labeled oligonucleotides to study the structure of either RNA-cleaving DNAzymes in complex with their RNA targets or modified DNAzymes with different functions and targets, in which deoxynucleotides are substituted by nitroxide-labeled nucleotides.

Single-molecule Detection of Ultrafast Biomolecular Dynamics with Nanophotonics.

Single-molecule Förster resonance energy transfer (FRET) is a versatile technique for probing the structure and dynamics of biomolecules even in heterogeneous ensembles. However, because of the limited fluorescence brightness per molecule and the relatively long fluorescence lifetimes, probing ultrafast structural dynamics in the nanosecond time scale has thus far been very challenging. Here, we demonstrate that nanophotonic fluorescence enhancement in zero-mode waveguides enables measurements of previously inaccessible low-nanosecond dynamics by dramatically improving time resolution and reduces data acquisition times by more than an order of magnitude. As a prototypical example, we use this approach to probe the dynamics of a short intrinsically disordered peptide that were previously inaccessible with single-molecule FRET measurements. We show that we are now able to detect the low-nanosecond correlations in this peptide, and we obtain a detailed interpretation of the underlying distance distributions and dynamics in conjunction with all-atom molecular dynamics simulations, which agree remarkably well with the experiments. We expect this combined approach to be widely applicable to the investigation of very rapid biomolecular dynamics.

How to Access the Cryo-EM Facility in KEK

In March 2018, KEK obtained a 200 kV cryogenic electron microscopy（cryo-EM; a Talos Arctica G2 with a Falcon 3EC direct electron detector）and prepared a pipeline for solving high-resolution structures of macromolecular biomolecules, such as proteins, DNA, and RNA. In October 2018, the cryo-EM facility in KEK opened to academic and industrial users. Our mission is three-fold：to provide cryo-EM machine time for external users, to support grid-prep and data collection（and single particle analysis, if needed）, and to help users acquire cryo-EM skills. One remarkable result is the single-particle analysis of an 860-kDa enzyme at 2.05 angstrom resolution, which suggested that we had established a proper protocol for cryo-EM operation and single-particle analysis. We will continue to support external users and carry out cryo-EM single particle analysis of macromolecular biomolecules.

Interpretation of EPR and optical spectra of Ni(II) ions in crystalline lattices at ambient temperature.

Many biologically important paramagnetic metal ions are characterized by electron paramagnetic resonance (EPR) spectroscopy to use as spin probes to investigate the structure and function of biomolecules. Though nickel(II) ions are an essential trace element and part of many biomolecules, the EPR properties are least understood. Herein, the EPR and optical absorption spectra measured at 300 K for Ni(II) ions diluted in two different diamagnetic hosts are investigated and reported. The EPR spectrum of a polycrystalline Ni/Mg(3-methylpyrazole)6 (ClO4 )2 [Ni/MMPC] shows two transitions at X-band frequency (~9.5GHz), suggesting the zero-field splitting parameter (D) is larger than the resonance field of the free electron (Ho ). This incomplete and complex spectrum is successfully analyzed to obtain EPR parameters. The EPR spectrum of the polycrystalline Ni/Zn(pyrazole)6 (NO3 )2 [Ni/ZPN] shows a triplet spectrum indicating D<Ho . A detailed analysis of single-crystal EPR data yielded the spin Hamiltonian parameters. The optical absorption spectra are deconvoluted to understand the symmetry of the coordination environment in the complex.

Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants

Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.