scholarly journals Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study

Soft Matter ◽  
2014 ◽  
Vol 10 (2) ◽  
pp. 290-302 ◽  
Author(s):  
Diana Fusco ◽  
Jeffrey J. Headd ◽  
Alfonso De Simone ◽  
Jun Wang ◽  
Patrick Charbonneau
Keyword(s):  
Protein Crystal ◽  
Crystal Contacts

scholarly journals Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase

IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 130-140 ◽  
Author(s):  
Margarita Dimova ◽  
Yancho D. Devedjiev
Keyword(s):  
Condensed Phase ◽  
Protein Structures ◽  
Van Der Waals Interactions ◽  
Protein Crystal ◽  
Crystal Formation ◽  
Conformational Entropy ◽  
Crystal Lattices ◽  
Crystal Contacts ◽  
First Time

Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.

scholarly journals TELSAM polymers accelerate crystallization of fused target proteins by stabilizing minimal crystal contacts and in the absence of direct inter-TELSAM contacts

2021 ◽  
Author(s):  
Supeshala Dilrukshi Sarath Nawarathnage ◽  
Sara Soleimani ◽  
Moriah H Mathis ◽  
Braydan D Bezzant ◽  
Diana T Ramírez ◽  
...  
Keyword(s):  
Protein Crystallization ◽  
Target Protein ◽  
Protein Crystal ◽  
Protein Fusion ◽  
Definitive Evidence ◽  
Helical Polymer ◽  
Crystal Contacts ◽  
Genetic Fusion ◽  
Direct Inter ◽  
Future Work

We extend investigation into the usefulness of genetic fusion to TELSAM polymers as an effective protein crystallization strategy. We tested various numbers of the target protein fused per turn of the TELSAM helical polymer and various TELSAM–target connection strategies. We provide definitive evidence that: 1. A TELSAM–target protein fusion can crystallize more rapidly than the same target protein alone, 2. TELSAM–target protein fusions can form well-ordered, diffracting crystals using either flexible or rigid TELSAM–target linkers, 3. Well-ordered crystals can be obtained when either 2 or 6 copies of the target protein are presented per turn of the TELSAM helical polymer, 4. The TELSAM polymers themselves need not directly contact one another in the crystal lattice, and 5. Fusion to TELSAM polymer confers immense avidity to stabilize exquisitely weak inter-target protein crystal contacts. We report features of TELSAM-target protein crystals and outline future work needed to define the requirements for reliably obtaining optimal crystals of TELSAM–target protein fusions.

scholarly journals Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study

2020 ◽  
Vol 1864 (2) ◽  
pp. 129418 ◽  
Author(s):  
Siqin Bala ◽  
Shoko Shinya ◽  
Arpita Srivastava ◽  
Marie Ishikawa ◽  
Atsushi Shimada ◽  
...  
Keyword(s):  
Protein Crystal ◽  
Flexible Loop ◽  
Contact Free ◽  
Crystal Contact

A case study on the treatment of protein SIRAS data

2014 ◽  
Vol 70 (10) ◽  
pp. 2686-2691 ◽  
Author(s):  
Deqiang Yao ◽  
Tao Zhang ◽  
Yao He ◽  
Pu Han ◽  
Maia Cherney ◽  
...  
Keyword(s):  
Direct Method ◽  
Direct Methods ◽  
Phase Model ◽  
Protein Crystal ◽  
Scattering Data ◽  
Anomalous Scattering ◽  
Data Set ◽  
Model Extension ◽  
Sad Phasing

A case study has been made on the treatment of the SIRAS (single isomorphous replacement with anomalous scattering) data of the originally unknown protein LegC3N. An alternative treatment has been proposed which led to improved results in this particular test case. The treatment involves iterative direct-method SAD (single-wavelength anomalous diffraction) phasing and direct-method-aided model completion, both of which are implanted in theIPCAS(Iterative Protein Crystal-structure Automatic Solution) pipeline. Apart from the experimental data, a simulated SIRAS data set for LegC3N with the derivative data truncated to 5.0 Å resolution has also been tested. SAD phasing and phase/model extension inPHENIXwithout direct methods failed to solve the structure using these simulated SIRAS data. However, the procedure proposed here involving direct methods in both SAD phasing and phase/model extension led to a nearly complete structure model. This shows the potential ability of treating SIRAS data with a derivative diffracting to lower resolution.

An Unconventional Mode of Protein Crystal Growth: Case Study Xylanase

2012 ◽  
Vol 12 (6) ◽  
pp. 2986-2993 ◽  
Author(s):  
Mike Sleutel ◽  
Alexander E. S. Van Driessche ◽  
Dominique Maes
Keyword(s):  
Crystal Growth ◽  
Protein Crystal ◽  
Protein Crystal Growth

scholarly journals Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 588
Author(s):  
Johannes Hermann ◽  
Daniel Bischoff ◽  
Phillip Grob ◽  
Robert Janowski ◽  
Dariusch Hekmat ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Interactions ◽  
Computational Study ◽  
Protein Crystallization ◽  
Lactobacillus Brevis ◽  
Protein Crystal ◽  
Crystal Formation ◽  
Contact Stability ◽  
Crystal Contacts ◽  
Energy Simulations

Protein crystallization can function as an effective method for protein purification or formulation. Such an application requires a comprehensive understanding of the intermolecular protein–protein interactions that drive and stabilize protein crystal formation to ensure a reproducible process. Using alcohol dehydrogenase from Lactobacillus brevis (LbADH) as a model system, we probed in our combined experimental and computational study the effect of residue substitutions at the protein crystal contacts on the crystallizability and the contact stability. Increased or decreased contact stability was calculated using molecular dynamics (MD) free energy simulations and showed excellent qualitative correlation with experimentally determined increased or decreased crystallizability. The MD simulations allowed us to trace back the changes to their physical origins at the atomic level. Engineered charge–charge interactions as well as engineered hydrophobic effects could be characterized and were found to improve crystallizability. For example, the simulations revealed a redesigning of a water mediated electrostatic interaction (“wet contact”) into a water depleted hydrophobic effect (“dry contact”) and the optimization of a weak hydrogen bonding contact towards a strong one. These findings explained the experimentally found improved crystallizability. Our study emphasizes that it is difficult to derive simple rules for engineering crystallizability but that free energy simulations could be a very useful tool for understanding the contribution of crystal contacts for stability and furthermore could help guide protein engineering strategies to enhance crystallization for technical purposes.

scholarly journals Multiple crystal forms ofN,N′-diacetylchitobiose deacetylase fromPyrococcus furiosus

2015 ◽  
Vol 71 (6) ◽  
pp. 657-662 ◽  
Author(s):  
Tsutomu Nakamura ◽  
Mayumi Niiyama ◽  
Wakana Hashimoto ◽  
Kurumi Ida ◽  
Manabu Abe ◽  
...  
Keyword(s):  
Complex Formation ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Pyrococcus Furiosus ◽  
Protein Crystal ◽  
Cadmium Complex ◽  
Crystal Forms ◽  
Cell Parameters ◽  
Distorted Octahedral ◽  
Crystal Contacts

NativeN,N′-diacetylchitobiose deacetylase fromPyrococcus furiosus(Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd—Se bond than the Cd—S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative.

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