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Article ; Online: X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals.

Soares, Alexei S / Caspar, Donald L D

2017 Volume 200, Issue 3, Page(s) 213–218

Abstract: X-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room ... ...

Abstract	X-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electrons inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(000), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(000) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75±12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.
MeSH term(s)	Crystallization ; Crystallography, X-Ray/methods ; Electrons ; Insulin/chemistry ; Solvents ; Temperature ; Trehalose/chemistry ; X-Ray Diffraction/methods
Chemical Substances	Insulin ; Solvents ; Trehalose (B8WCK70T7I)
Language	English
Publishing date	2017-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2017.08.004
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Article ; Online: Structural analysis and biochemical properties of laccase enzymes from two Pediococcus species.

Olmeda, Isidoro / Casino, Patricia / Collins, Robert E / Sendra, Ramón / Callejón, Sara / Huesa, Juanjo / Soares, Alexei S / Ferrer, Sergi / Pardo, Isabel

Microbial biotechnology

2021 Volume 14, Issue 3, Page(s) 1026–1043

Abstract: Prokaryotic laccases are emergent biocatalysts. However, they have not been broadly found and characterized in bacterial organisms, especially in lactic acid bacteria. Recently, a prokaryotic laccase from the lactic acid bacterium Pediococcus ... ...

Abstract	Prokaryotic laccases are emergent biocatalysts. However, they have not been broadly found and characterized in bacterial organisms, especially in lactic acid bacteria. Recently, a prokaryotic laccase from the lactic acid bacterium Pediococcus acidilactici 5930, which can degrade biogenic amines, was discovered. Thus, our study aimed to shed light on laccases from lactic acid bacteria focusing on two Pediococcus laccases, P. acidilactici 5930 and Pediococcus pentosaceus 4816, which have provided valuable information on their biochemical activities on redox mediators and biogenic amines. Both laccases are able to oxidize canonical substrates as ABTS, ferrocyanide and 2,6-DMP, and non-conventional substrates as biogenic amines. With ABTS as a substrate, they prefer an acidic environment and show sigmoidal kinetic activity, and are rather thermostable. Moreover, this study has provided the first structural view of two lactic acid bacteria laccases, revealing new structural features not seen before in other well-studied laccases, but which seem characteristic for this group of bacteria. We believe that understanding the role of laccases in lactic acid bacteria will have an impact on their biotechnological applications and provide a framework for the development of engineered lactic acid bacteria with enhanced properties.
MeSH term(s)	Bacteria/metabolism ; Laccase/metabolism ; Oxidation-Reduction ; Pediococcus/metabolism ; Prokaryotic Cells/metabolism
Chemical Substances	Laccase (EC 1.10.3.2)
Language	English
Publishing date	2021-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2406063-X
ISSN	1751-7915 ; 1751-7915
ISSN (online)	1751-7915
ISSN	1751-7915
DOI	10.1111/1751-7915.13751
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Article ; Online: Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant.

Andi, Babak / Soares, Alexei S / Shi, Wuxian / Fuchs, Martin R / McSweeney, Sean / Liu, Qun

Acta crystallographica. Section F, Structural biology communications

2019 Volume 75, Issue Pt 9, Page(s) 616–624

Abstract: The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals ... ...

Abstract	The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an R
MeSH term(s)	Acyltransferases/chemistry ; Amidohydrolases/chemistry ; Arabidopsis/enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Models, Molecular
Chemical Substances	Acyltransferases (EC 2.3.-) ; dihydrolipoamide succinyltransferase (EC 2.3.1.61) ; Amidohydrolases (EC 3.5.-) ; amidase (EC 3.5.1.4)
Language	English
Publishing date	2019-08-29
Publishing country	United States
Document type	Journal Article
ISSN	2053-230X
ISSN (online)	2053-230X
DOI	10.1107/S2053230X19011488
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Article ; Online: A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs.

Nguyen, Thu / Phan, Kim L / Kozakov, Dima / Gabelli, Sandra B / Kreitler, Dale F / Andrews, Lawrence C / Jakoncic, Jean / Sweet, Robert M / Soares, Alexei S / Bernstein, Herbert J

Acta crystallographica. Section D, Structural biology

2022 Volume 78, Issue Pt 3, Page(s) 268–277

Abstract: One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in ...

Abstract	One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.
MeSH term(s)	Models, Molecular ; Molecular Conformation ; Molecular Structure ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2022-02-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798321013425
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Article ; Online: Serial crystallography with multi-stage merging of thousands of images.

Soares, Alexei S / Yamada, Yusuke / Jakoncic, Jean / McSweeney, Sean / Sweet, Robert M / Skinner, John / Foadi, James / Fuchs, Martin R / Schneider, Dieter K / Shi, Wuxian / Andi, Babak / Andrews, Lawrence C / Bernstein, Herbert J

Acta crystallographica. Section F, Structural biology communications

2022 Volume 78, Issue Pt 7, Page(s) 281–288

Abstract: KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support ... ...

Abstract	KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.
MeSH term(s)	Algorithms ; Cluster Analysis ; Crystallography, X-Ray ; Proteins/chemistry ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2022-07-04
Publishing country	United States
Document type	Journal Article
ISSN	2053-230X
ISSN (online)	2053-230X
DOI	10.1107/S2053230X22006422
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Article: The use of haptic interfaces and web services in crystallography: an application for a 'screen to beam' interface.

Bruno, Andrew E / Soares, Alexei S / Owen, Robin L / Snell, Edward H

Journal of applied crystallography

2016 Volume 49, Issue Pt 6, Page(s) 2082–2090

Abstract: Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. The work presented here illustrates the application of a haptic interface to crystallization ... ...

Abstract	Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. The work presented here illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from 'point and click' to 'touch and share', where results can be selected, annotated and discussed collaboratively. In the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting information can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient 'screen to beam' approach. The application is not limited to the area of crystallization screening; 'touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.
Language	English
Publishing date	2016-11-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2020879-0
ISSN	1600-5767 ; 0021-8898
ISSN (online)	1600-5767
ISSN	0021-8898
DOI	10.1107/S160057671601431X
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Article ; Online: Crystallographic characterization of the nitric oxide derivative of R-state human hemoglobin.

Yi, Jun / Soares, Alexei S / Richter-Addo, George B

Nitric oxide : biology and chemistry

2014 Volume 39, Page(s) 46–50

Abstract: Nitric oxide (NO) is a signaling agent that is biosynthesized in vivo. NO binds to the heme center in human hemoglobin (Hb) to form the HbNO adduct. This reaction of NO with Hb has been studied for many decades. Of continued interest has been the effect ... ...

Abstract	Nitric oxide (NO) is a signaling agent that is biosynthesized in vivo. NO binds to the heme center in human hemoglobin (Hb) to form the HbNO adduct. This reaction of NO with Hb has been studied for many decades. Of continued interest has been the effect that the bound NO ligand has on the geometrical parameters of the resulting heme-NO active site. Although the crystal structure of a T-state human HbNO complex has been published previously, that of the high affinity R-state HbNO derivative has not been reported to date. We have crystallized and solved the three-dimensional X-ray structure of R-state human HbNO to 1.90 Å resolution. The differences in the FeNO bond parameters and H-bonding patterns between the α and β subunits contribute to understanding of the observed enhanced stability of the α(FeNO) moieties relative to the β(FeNO) moieties in human R-state HbNO.
MeSH term(s)	Crystallography, X-Ray ; Glycated Hemoglobin A/chemistry ; Glycated Hemoglobin A/metabolism ; Humans ; Molecular Structure ; Nitric Oxide/chemistry ; Nitric Oxide/metabolism ; Protein Binding
Chemical Substances	Glycated Hemoglobin A ; hemoglobin A, glycosylated-nitric oxide complex ; Nitric Oxide (31C4KY9ESH)
Language	English
Publishing date	2014-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1362794-6
ISSN	1089-8611 ; 1089-8603
ISSN (online)	1089-8611
ISSN	1089-8603
DOI	10.1016/j.niox.2014.04.001
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Zs.A 4677: Show issues

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Article ; Online: Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.

Andi, Babak / Kumaran, Desigan / Kreitler, Dale F / Soares, Alexei S / Keereetaweep, Jantana / Jakoncic, Jean / Lazo, Edwin O / Shi, Wuxian / Fuchs, Martin R / Sweet, Robert M / Shanklin, John / Adams, Paul D / Schmidt, Jurgen G / Head, Martha S / McSweeney, Sean

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12197

Abstract: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to ... ...

Abstract	Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M
MeSH term(s)	Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Coronavirus 3C Proteases ; Cysteine Endopeptidases/metabolism ; Hepacivirus/metabolism ; Humans ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; SARS-CoV-2 ; Viral Nonstructural Proteins/genetics
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Viral Nonstructural Proteins ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2022-07-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-15930-z
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Article ; Online: The structure of NAD

The Journal of biological chemistry

2023 Volume 299, Issue 11, Page(s) 105290

Abstract: Toll-like and interleukin-1/18 receptor/resistance (TIR) domain-containing proteins function as important signaling and immune regulatory molecules. TIR domain-containing proteins identified in eukaryotic and prokaryotic species also exhibit NAD+ ... ...

Abstract	Toll-like and interleukin-1/18 receptor/resistance (TIR) domain-containing proteins function as important signaling and immune regulatory molecules. TIR domain-containing proteins identified in eukaryotic and prokaryotic species also exhibit NAD+ hydrolase activity in select bacteria, plants, and mammalian cells. We report the crystal structure of the Acinetobacter baumannii TIR domain protein (AbTir-TIR) with confirmed NAD
MeSH term(s)	Acinetobacter baumannii/genetics ; Acinetobacter baumannii/metabolism ; Bacteria/metabolism ; Bacterial Proteins/metabolism ; Deuterium ; Hydrolases/metabolism ; Mammals/metabolism ; NAD/metabolism ; Protein Domains
Chemical Substances	Bacterial Proteins ; Deuterium (AR09D82C7G) ; Hydrolases (EC 3.-) ; NAD (0U46U6E8UK)
Language	English
Publishing date	2023-09-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105290
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Uc I Zs.108: Show issues

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Article: Best practices for high data-rate macromolecular crystallography (HDRMX).

Bernstein, Herbert J / Andrews, Lawrence C / Diaz, Jorge A / Jakoncic, Jean / Nguyen, Thu / Sauter, Nicholas K / Soares, Alexei S / Wei, Justin Y / Wlodek, Maciej R / Xerri, Mario A

Structural dynamics (Melville, N.Y.)

2020 Volume 7, Issue 1, Page(s) 14302

Abstract: In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the ... ...

Abstract	In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.
Language	English
Publishing date	2020-01-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2758684-4
ISSN	2329-7778
ISSN	2329-7778
DOI	10.1063/1.5128498
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