scholarly journals Helical ensembles out-perform ideal helices in Molecular Replacement

2020 ◽  
Author(s):  
Filomeno Sánchez Rodríguez ◽  
Adam J. Simpkin ◽  
Owen R. Davies ◽  
Ronan M. Keegan ◽  
Daniel J. Rigden
Keyword(s):  
Coiled Coil ◽  
Structural Similarity ◽  
Structural Heterogeneity ◽  
Molecular Replacement ◽  
Number Of Solutions ◽  
Unknown Protein ◽  
Small Ideal ◽  
Alternative Approaches ◽  
Helical Proteins ◽  
Time Required

AbstractThe conventional approach in molecular replacement (MR) is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterised families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high albeit local structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolution. Here we explore the performance of libraries of helical ensembles created by clustering helical segments. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. We observed a 30% increase in the number of solutions obtained by AMPLE when using this new set of ensembles compared to performance with ideal helices. The boost of performance was notable across three different folds: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction of the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the “helical ensembles” mode.

scholarly journals Helical ensembles outperform ideal helices in molecular replacement

2020 ◽  
Vol 76 (10) ◽  
pp. 962-970
Author(s):  
Filomeno Sánchez Rodríguez ◽  
Adam J. Simpkin ◽  
Owen R. Davies ◽  
Ronan M. Keegan ◽  
Daniel J. Rigden
Keyword(s):  
Coiled Coil ◽  
Structural Similarity ◽  
Structural Heterogeneity ◽  
Molecular Replacement ◽  
Number Of Solutions ◽  
Unknown Protein ◽  
Small Ideal ◽  
Alternative Approaches ◽  
Helical Proteins ◽  
Time Required

The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the `helical ensembles' mode.

scholarly journals Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill

2018 ◽  
Vol 115 (34) ◽  
pp. E7905-E7913 ◽  
Author(s):  
Xingcheng Lin ◽  
Jeffrey K. Noel ◽  
Qinghua Wang ◽  
Jianpeng Ma ◽  
José N. Onuchic
Keyword(s):  
Viral Entry ◽  
Large Scale ◽  
Coiled Coil ◽  
Structural Rearrangement ◽  
Structural Heterogeneity ◽  
Host Cells ◽  
Fusion Peptides ◽  
Influenza Hemagglutinin ◽  
Loop Region ◽  
Coil Transition

Influenza hemagglutinin (HA) mediates viral entry into host cells through a large-scale conformational rearrangement at low pH that leads to fusion of the viral and endosomal membranes. Crystallographic and biochemical data suggest that a loop-to-coiled-coil transition of the B-loop region of HA is important for driving this structural rearrangement. However, the microscopic picture for this proposed “spring-loaded” movement is missing. In this study, we focus on understanding the transition of the B loop and perform a set of all-atom molecular dynamics simulations of the full B-loop trimeric structure with the CHARMM36 force field. The free-energy profile constructed from our simulations describes a B loop that stably folds half of the postfusion coiled coil in tens of microseconds, but the full coiled coil is unfavorable. A buried hydrophilic residue, Thr59, is implicated in destabilizing the coiled coil. Interestingly, this conserved threonine is the only residue in the B loop that strictly differentiates between the group 1 and 2 HA molecules. Microsecond-scale constant temperature simulations revealed that kinetic traps in the structural switch of the B loop can be caused by nonnative, intramonomer, or intermonomer β-sheets. The addition of the A helix stabilized the postfusion state of the B loop, but introduced the possibility for further β-sheet structures. Overall, our results do not support a description of the B loop in group 2 HAs as a stiff spring, but, rather, it allows for more structural heterogeneity in the placement of the fusion peptides during the fusion process.

scholarly journals Transmission of Still Images Using Low-Complexity Analog Joint Source-Channel Coding

Sensors ◽  
2019 ◽  
Vol 19 (13) ◽  
pp. 2932 ◽  
Author(s):  
Jose Balsa ◽  
Tomás Domínguez-Bolaño ◽  
Óscar Fresnedo ◽  
José A. García-Naya ◽  
Luis Castedo
Keyword(s):  
Channel Coding ◽  
Additive White Gaussian Noise ◽  
Structural Similarity ◽  
Low Complexity ◽  
Surveillance Systems ◽  
Still Images ◽  
Joint Source Channel Coding ◽  
Visual Degradation ◽  
Time Required ◽  
Source Channel Coding

An analog joint source-channel coding (JSCC) system designed for the transmission of still images is proposed and its performance is compared to that of two digital alternatives which differ in the source encoding operation: Joint Photographic Experts Group (JPEG) and JPEG without entropy coding (JPEGw/oEC), respectively, both relying on an optimized channel encoder–modulator tandem. Apart from a visual comparison, the figures of merit considered in the assessment are the structural similarity (SSIM) index and the time required to transmit an image through additive white Gaussian noise (AWGN) and Rayleigh channels. This work shows that the proposed analog system exhibits a performance similar to that of the digital scheme based on JPEG compression with a noticeable better visual degradation to the human eye, a lower computational complexity, and a negligible delay. These results confirm the suitability of analog JSCC for the transmission of still images in scenarios with severe constraints on power consumption, computational capabilities, and for real-time applications. For these reasons the proposed system is a good candidate for surveillance systems, low-constrained devices, Internet of things (IoT) applications, etc.

scholarly journals Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

2015 ◽  
Vol 112 (29) ◽  
pp. E3806-E3815 ◽  
Author(s):  
Keenan C. Taylor ◽  
Massimo Buvoli ◽  
Elif Nihal Korkmaz ◽  
Ada Buvoli ◽  
Yuqing Zheng ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Structural Similarity ◽  
Thick Filament ◽  
Biological Properties ◽  
Stable States ◽  
Filament Assembly ◽  
High Structural Similarity ◽  
Heptad Repeats ◽  
Local Relaxation ◽  
Molecular Hinge

The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

scholarly journals Using Phaser and ensembles to improve the performance of SIMBAD

2020 ◽  
Vol 76 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Adam J. Simpkin ◽  
Felix Simkovic ◽  
Jens M. H. Thomas ◽  
Martin Savko ◽  
Andrey Lebedev ◽  
...  
Keyword(s):  
Model Identification ◽  
Structural Similarity ◽  
Test Cases ◽  
Target Sequence ◽  
Molecular Replacement ◽  
Search Models ◽  
Termination Criteria ◽  
Alternative Approach ◽  
The Relationship ◽  
Rotation Function

The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.

scholarly journals Comparative Judgement for Linking Two Existing Scales

2021 ◽  
Vol 6 ◽  
Author(s):  
Tom Benton
Keyword(s):  
Test Equating ◽  
Comparative Judgement ◽  
Test Linking ◽  
Educational Assessments ◽  
Alternative Approaches ◽  
Time Required

This article describes an efficient way of using comparative judgement to calibrate scores from different educational assessments against one another (a task often referred to as test linking or equating). The context is distinct from other applications of comparative judgement as there is no need to create a new achievement scale using a Bradley-Terry model (or similar). The proposed method takes advantage of this fact to include evidence from the largest possible number of examples of students’ performances on the separate assessments whilst keeping the amount of time required from expert judges as low as possible. The paper describes the method and shows, via simulation, how it achieves greater accuracy than alternative approaches to the use of comparative judgement for test equating or linking.

scholarly journals Crystal structure of theMSMEG_4306gene product fromMycobacterium smegmatis

2018 ◽  
Vol 74 (3) ◽  
pp. 166-173
Author(s):  
Adarsh Kumar ◽  
Subramanian Karthikeyan
Keyword(s):  
Crystal Structure ◽  
Coiled Coil ◽  
Structural Similarity ◽  
Data Bank ◽  
Zinc Ion ◽  
Terminal Region ◽  
Amino Acid Residues ◽  
Secretion Systems ◽  
C Terminus ◽  
Zinc Ribbon

TheMSMEG_4306gene fromMycobacterium smegmatisencodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 fromChlamydia trachomatisand HP0958 fromHelicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306. Based on comparative analysis, it is predicted that MSMEG_4306 may be involved in secretion systems, possibly by interacting with multiple proteins or nucleic acids.

Sovereign Insolvency and International Legal Order

2009 ◽  
Vol 11 (3) ◽  
pp. 307-326 ◽  
Author(s):  
Maria Chiara Malaguti
Keyword(s):  
International Law ◽  
Financial Crises ◽  
Sovereign Debt ◽  
Legal Order ◽  
International Level ◽  
Number Of Solutions ◽  
Present Contribution ◽  
International Legal Order ◽  
Alternative Approaches ◽  
The Imf

AbstractThe rescue of States in a financial crises has been classically managed by way of official lending, mainly managed by the IMF, where international law played the major role. In most recent cases, to the contrary, this has mainly become a private law issue: since debtors, including sovereign, undertake exposure on a contractual basis, repayment or negotiation of the debt is governed by such same contract. These present a number of pitfalls and shortcomings which have been tried to be solved by a number of solutions. Each of them, however, not only is not fully satisfactory, but cannot take into account all interests at stake. To this end, a number of projects have been elaborated, to regulate the matter at the international level, starting from the Sovereign Debt Restructuring Mechanism of the IMF to other proposals of international bankruptcy codes, none of which has been adopted. The present contribution analyses the consequences of these proposals on sovereignty and how alternative approaches could better respond to international stances while respecting private tools.

scholarly journals Combinatorial use of disulfide bridges and native sulfur-SAD phasing for rapid structure determination of coiled-coils

2018 ◽  
Vol 38 (5) ◽  
Author(s):  
Sebastian H.W. Kraatz ◽  
Sarah Bianchi ◽  
Michel O. Steinmetz
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Molecular Replacement ◽  
Disulfide Bridges ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Protein Interaction ◽  
Eukaryotic Proteins ◽  
Sad Phasing

Coiled-coils are ubiquitous protein–protein interaction motifs found in many eukaryotic proteins. The elongated, flexible and often irregular nature of coiled-coils together with their tendency to form fibrous arrangements in crystals imposes challenges on solving the phase problem by molecular replacement. Here, we report the successful combinatorial use of native and rational engineered disulfide bridges together with sulfur-SAD phasing as a powerful tool to stabilize and solve the structure of coiled-coil domains in a straightforward manner. Our study is a key example of how modern sulfur SAD combined with mutagenesis can help to advance and simplify the structural study of challenging coiled-coil domains by X-ray crystallography.

De novo design of α-helical proteins: basic research to medical applications

1996 ◽  
Vol 74 (2) ◽  
pp. 133-154 ◽  
Author(s):  
Robert S. Hodges
Keyword(s):  
Protein Folding ◽  
De Novo ◽  
Coiled Coil ◽  
Basic Research ◽  
De Novo Design ◽  
Coiled Coils ◽  
Medical Applications ◽  
Dimerization Domain ◽  
Recombinant Peptides ◽  
Helical Proteins

The two-stranded α-helical coiled-coil is a universal dimerization domain used by nature in a diverse group of proteins. The simplicity of the coiled-coil structure makes it an ideal model system to use in understanding the fundamentals of protein folding and stability and in testing the principles of de novo design. The issues that must be addressed in the de novo design of coiled-coils for use in research and medical applications are (i) controlling parallel versus antiparallel orientation of the polypeptide chains, (ii) controlling the number of helical strands in the assembly (iii) maximizing stability of homodimers or heterodimers in the shortest possible chain length that may require the engineering of covalent constraints, and (iv) the ability to have selective heterodimerization without homodimerization, which requires a balancing of selectivity versus affinity of the dimerization strands. Examples of our initial inroads in using this de novo design motif in various applications include: heterodimer technology for the detection and purification of recombinant peptides and proteins; a universal dimerization domain for biosensors; a two-stage targeting and delivery system; and coiled-coils as templates for combinatorial helical libraries for basic research and drug discovery and as synthetic carrier molecules. The universality of this dimerization motif in nature suggests an endless number of possibilities for its use in de novo design, limited only by the creativity of peptide–protein engineers.Key words: de novo design of proteins, α-helical coiled-coils, protein folding, protein stability, dimerization domain, dimerization motif.

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