Temperature artifacts in protein structures bias ligand-binding predictions

Bradford, S.Y.C.; Khoury, Léa El; Ge, Yunhui; Osato, Meghan; Mobley, David L.; Fischer, Marcus

doi:10.1039/d1sc02751d

Cited by 29 publications

(52 citation statements)

References 96 publications

(193 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Neutron macromolecular crystallography is the technique of choice for determining the positions of hydrogen atoms and the protonation states of active groups 18 – 21 that are involved in the catalytic activity of enzymes or the binding of a ligand to a macromolecule 22 – 25 . Moreover, neutrons do not cause any radiation damage to the biological sample so the structure determination and data collection can be performed at room temperature (RT), giving a more accurate view of local flexibility and water mobility at biologically relevant temperatures 26 , 27 .…”

Section: Introductionmentioning

confidence: 99%

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

et al. 2022

View full text Add to dashboard Cite

The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low-barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.

show abstract

Section: Introductionmentioning

confidence: 99%

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

et al. 2022

View full text Add to dashboard Cite

show abstract

“…They collected the data at ambient temperature using femtosecond X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (Hyogo, Japan). More recently Bradford et al found the conformational changes in response to temperature in the T4 lysozyme L99A cavity by single crystal synchrotron X-ray crystallography [11]. They collected diffraction data at both ambient temperature (278 K) and cryogenic temperature (100 K) using synchrotron X-ray diffraction at the Advanced Photon Source (Lemont, IL, USA) beamline ID-24.…”

Section: Introductionmentioning

confidence: 99%

Precipitant-Free Crystallization of Lysozyme and Glucose Isomerase by Drying

et al. 2022

View full text Add to dashboard Cite

Protein crystallization is usually conducted by using precipitants, although the “salting-out” phenomenon is still unclear and complex. Moreover, the addition of precipitants sometimes results in irreversible disordered precipitation of protein molecules. Although precipitant-free lysozyme crystals obtained by centrifugal concentration showed significant changes in three-dimensional structure compared to the structure of salted-out crystals, it was rather difficult to mount crystals from a viscous dense liquid phase after centrifugal concentration, and the quality of the crystals often deteriorated during the mounting process. Here we present novel precipitant-free crystallization methods, which were effective for lysozyme and glucose isomerase. Tetragonal lysozyme crystals were successfully crystallized in a glass capillary simply by drying highly concentrated lysozyme solution in the presence of 0.01 M hydrochloric acid without using any precipitants. Glucose isomerase dissolved in ultra-pure water was also successfully crystallized in hanging drops by drying highly concentrated solution under low-humidity conditions. Oscillation images of the obtained crystals were safely collected without handling; they clearly indicated the crystals had a tetragonal form for lysozyme and an orthorhombic form for glucose isomerase, and their lattice parameters are similar to those of previously reported crystals obtained by salting-out methods.

show abstract

“…In addition, cryogenic temperature may perturb the overall protein backbone fold [26]. Therefore, studies have recommended greater caution when referring only to cryogenic structures [24, 25]. In order to reveal the underpinnings of this elegant system, it is essential to examine the details of structural dynamics of the apo- state at near-physiological temperatures which are currently a missing reference point.…”

Section: Introductionmentioning

confidence: 99%

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Ayan

Yüksel

Destan

et al. 2021

Preprint

View full text Add to dashboard Cite

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

show abstract

Temperature artifacts in protein structures bias ligand-binding predictions

Abstract: X-ray crystallography is the gold standard to resolve conformational ensembles that are significant for protein function, ligand discovery, and computational methods development. However, relevant conformational states may be missed at...

Cited by 29 publications

References 96 publications

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding

Precipitant-Free Crystallization of Lysozyme and Glucose Isomerase by Drying

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Contact Info

Product

Resources

About