Extending the novel |ρ|-based phasing algorithm to the solution of anomalous scattering substructures from SAD data of protein crystals

Rius, Jordi; Torrelles, X.

doi:10.1107/s2053273322008622

Cited by 3 publications

(2 citation statements)

References 35 publications

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“…Also, the extremely intense radiation of X-ray free-electron lasers (XFEL) is suitable for SAD phasing with protein microcrystals [ 59 ]. This method is constantly being improved, e.g., with the SAD-SMAR algorithm, which facilitates to determine the anomalous scattering substructure in a highly efficient manner [ 60 ]. Currently, about 30% of all crystal structures are solved by experimental phasing methods; the rest only requires molecular replacement with a related protein model [ 61 ].…”

Section: Methods For the Incorporation Of Ncaas In Peptides And Proteinsmentioning

confidence: 99%

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

Goettig,

Koch,

Budisa

2023

IJMS

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All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.

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Section: Methods For the Incorporation Of Ncaas In Peptides And Proteinsmentioning

confidence: 99%

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

Goettig,

Koch,

Budisa

2023

IJMS

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“…[13] This method can improve the signal-to-noise ratio (SNR) of the difference Patterson map, which facilitates real space-based substructure determination, such as RSPS program. [14] In 2022, Rius and Torrelles developed a SAD-SAMR algorithm [15] that has been implemented in a modified version of XLENS v1. [16] This algorithm is a density-based phasing algorithm that incorporates a peaknessenhancing ipp (inner-pixel preservation) procedure, which features two Fourier iterations into one phase refinement cycle.…”

Section: Introductionmentioning

confidence: 99%

DSAS: A new macromolecular substructure solution program based on the modified phase-retrieval algorithm

Fu 付,

Tan 谭,

Geng 耿

et al. 2024

Chinese Phys. B

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Considering the pivotal role of single-wavelength anomalous diffraction (SAD) in macromolecular crystallography, our objective was to introduce DSAS, a novel program designed for efficient anomalous scattering substructure determination. DSAS stands out with its core components: a modified phase-retrieval algorithm and automated parameter tuning. The software boasts an intuitive graphical user interface (GUI), facilitating seamless input of essential data and real-time monitoring. Extensive testing on DSAS has involved diverse datasets, encompassing proteins, nucleic acids, and various anomalous scatters such as sulfur (S), selenium (Se), metals, and halogens. The results confirm DSAS's exceptional performance in accurately determining heavy atom positions, making it a highly effective tool in the field.

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The general equation of δ direct methods and the novel SMAR algorithm residuals using the absolute value of ρ and the zero conversion of negative ripples

Rius

2025

Acta Crystallogr A Found Adv

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The general equation δ M (r) = ρ(r) + g(r) of the δ direct methods (δ-GEQ) is established which, when expressed in the form δ M (r) − ρ(r) = g(r), is used in the SMAR phasing algorithm [Rius (2020). Acta Cryst A76, 489–493]. It is shown that SMAR is based on the alternating minimization of the two residuals R ρ(χ) = ∫ V [ρ(χ) − ρ(Φ)s ρ]2 dV and R δ(Φ) = ∫ V m ρ[δ M (χ) − ρ(Φ)s ρ]2 dV in each iteration of the algorithm by maximizing the respective S ρ(Φ) and S δ(Φ) sum functions. While R ρ(χ) converges to zero, R δ(Φ) converges, as predicted by the theory, to a positive quantity. These two independent residuals combine δ M and ρ each with |ρ| while keeping the same unknowns, leading to overdetermination for diffraction data extending to atomic resolution. At the beginning of a SMAR phase refinement, the zero part of the m ρ mask [resulting from the zero conversion of the slightly negative ρ(Φ) values] occupies ∼50% of the unit-cell volume and increases by ∼5% when convergence is reached. The effects on the residuals of the two SMAR phase refinement modes, i.e. only using density functions (slow mode) supplemented by atomic constraints (fast mode), are discussed in detail. Due to its architecture, the SMAR algorithm is particularly well suited for Deep Learning. Another way of using δ-GEQ is by solving it in the form ρ(r) = δ M (r) − g(r), which provides a simple new derivation of the already known δ M tangent formula, the core of the δ recycling phasing algorithm [Rius (2012). Acta Cryst. A68, 399–400]. The nomenclature used here is: (i) Φ is the set of φ structure factor phases of ρ to be refined; (ii) δ M (χ) = FT−1{c(|E| − 〈|E|〉)×exp(iα)} with χ = {α}, the set of phases of |ρ| and c = scaling constant; (iii) m ρ = mask, being either 0 or 1; s ρ is 1 or −1 depending on whether ρ(Φ) is positive or negative.

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Extending the novel |ρ|-based phasing algorithm to the solution of anomalous scattering substructures from SAD data of protein crystals

Cited by 3 publications

References 35 publications

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

DSAS: A new macromolecular substructure solution program based on the modified phase-retrieval algorithm

The general equation of δ direct methods and the novel SMAR algorithm residuals using the absolute value of ρ and the zero conversion of negative ripples

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