Sahir Khurshid

Protein crystallization facilitated by molecularly imprinted polymers

We present a previously undescribed initiative and its application, namely the design of molecularly imprinted polymers (MIPs) for producing protein crystals that are essential for determining high-resolution 3D structures of proteins. MIPs, also referred to as “smart materials,” are made to contain cavities capable of rebinding protein; thus the fingerprint of the protein created on the polymer allows it to serve as an ideal template for crystal formation. We have shown that six different MIPs induced crystallization of nine proteins, yielding crystals in conditions that do not give crystals otherwise. The incorporation of MIPs in screening experiments gave rise to crystalline hits in 8–10% of the trials for three target proteins. These hits would have been missed using other known nucleants. MIPs also facilitated the formation of large single crystals at metastable conditions for seven proteins. Moreover, the presence of MIPs has led to faster formation of crystals in all cases where crystals would appear eventually and to major improvement in diffraction in some cases. The MIPs were effective for their cognate proteins and also for other proteins, with size compatibility being a likely criterion for efficacy. Atomic force microscopy (AFM) measurements demonstrated specific affinity between the MIP cavities and a protein-functionalized AFM tip, corroborating our hypothesis that due to the recognition of proteins by the cavities, MIPs can act as nucleation-inducing substrates (nucleants) by harnessing the proteins themselves as templates.

Porous nucleating agents for protein crystallization

Solving the structure of proteins is pivotal to achieving success in rational drug design and in other biotechnological endeavors. The most powerful method for determining the structure of proteins is X-ray crystallography, which relies on the availability of high-quality crystals. However, obtaining such crystals is a major hurdle. Nucleation is the crucial prerequisite step, which requires overcoming an energy barrier. The presence in a protein solution of a nucleant, a solid or a semiliquid substance that facilitates overcoming that barrier allows crystals to grow under ideal conditions, paving the way for the formation of high-quality crystals. The use of nucleants provides a unique means for optimizing the diffraction quality of crystals, as well as for discovering new crystallization conditions. We present a protocol for controlling the nucleation of protein crystals that is applicable to a wide variety of nucleation-inducing substances. Setting up crystallization trials using these nucleating agents takes an additional few seconds compared with conventional setup, and it can accelerate crystallization, which typically takes several days to months.

Heterogeneous nucleation of protein crystals using nanoporous gold nucleants

We present a theory and experiments that help clarify the origin of the effectiveness of nanoporous substrates in the heterogeneous nucleation of protein crystals. The central idea tested here is that when a substrate (or “nucleant”) possesses pores of the order of the hydrodynamical radius of a protein, then the entropic penalty associated with nucleating a protein crystal on that surface may be alleviated. Model experiments using lysozyme and nanoporous gold (NPG) substrates suggest that there is indeed a reduction in the entropy associated with creating critical nuclei, but the magnitude of the reduction is small. Taken together with further examination of protein crystallization with NPG nucleants using four other proteins, our aggregate results suggest that surface chemistry and surface area effects play the dominant role in nucleation when using these nanoporous nucleants.

Automated seeding for the optimization of crystal quality

With the advent of structural genomics a variety of crystallization techniques have been automated and applied to high-throughput pipelines, yet seeding, which is the most common and successful optimization method, is still being performed predominantly manually. The aim of this study was to devise simple automated seeding techniques that can be applied in a routine manner using existing robots and not requiring special tools. Two alternative protocols for automated seeding experiments are described. One involves the delivery of microcrystals from stock to target wells using the robot dispensing tip as a seeding tool. The second harnesses an animal whisker as the seeding tool. Larger and better ordered crystals were obtained using both techniques.

An investigation into the protonation states of the C1 domain of cardiac myosin-binding protein C

Myosin-binding protein C (MyBP-C) is a myofibril-associated protein found in cardiac and skeletal muscle. The cardiac isoform (cMyBP-C) is subject to reversible phosphorylation and the surface-charge state of the protein is of keen interest with regard to understanding the inter-protein interactions that are implicated in its function. Diffraction data from the C1 domain of cMyBP-C were extended to 1.30 A resolution, where the of the diffraction data crosses 2.0, using intense synchrotron radiation. The protonation-state determinations were not above 2sigma (the best was 1.81sigma) and therefore an extrapolation is given, based on 100% data completeness and the average DPI, that a 3sigma determination could be possible if X-ray data could be measured to 1.02 A resolution. This might be possible via improved crystallization or multiple sample evaluation, e.g. using robotics or a yet more intense/collimated X-ray beam or combinations thereof. An alternative would be neutron protein crystallography at 2 A resolution, where it is estimated that for the unit-cell volume of the cMyBP-C C1 domain crystal a crystal volume of 0.10 mm3 would be needed with fully deuterated protein on LADI III. These efforts would optimally be combined in a joint X-ray and neutron model refinement.

Exploring Carbon Nanomaterial Diversity for Nucleation of Protein Crystals.

Controlling crystal nucleation is a crucial step in obtaining high quality protein crystals for structure determination by X-ray crystallography. Carbon nanomaterials (CNMs) including carbon nanotubes, graphene oxide, and carbon black provide a range of surface topographies, porosities and length scales; functionalisation with two different approaches, gas phase radical grafting and liquid phase reductive grafting, provide routes to a range of oligomer functionalised products. These grafted materials, combined with a range of controls, were used in a large-scale assessment of the effectiveness for protein crystal nucleation of 20 different carbon nanomaterials on five proteins. This study has allowed a direct comparison of the key characteristics of carbon-based nucleants: appropriate surface chemistry, porosity and/or roughness are required. The most effective solid system tested in this study, carbon black nanoparticles functionalised with poly(ethylene glycol) methyl ether of mean molecular weight 5000, provides a novel highly effective nucleant, that was able to induce crystal nucleation of four out of the five proteins tested at metastable conditions.

Automating the application of smart materials for protein crystallization.

The first semi-liquid, non-protein nucleating agent for automated protein crystallization trials is described. This ‘smart material’ is demonstrated to induce crystal growth and will provide a simple, cost-effective tool for scientists in academia and industry.

Upside-down protein crystallization designing microbatch experiments for microgravity

Abstract:  The benefits of protein crystal growth in microgravity are well documented. The crystallization vessels currently employed for microgravity crystallization are far from optimal with regards to cost, sample volume, size, and ease of use. The use of microbatch experiments is a favorable alternative in each respect: 96 experiments of 0.5–2 μL volumes can be performed in a single microtiter tray measuring 5 × 8 cm and costing ££1 sterling each. To date, the use of microbatch has not been pursued on account of concerns of oil leakage. To address this issue, a novel approach to microbatch crystallization experiments is described, where the microbatch plates are inverted throughout the duration of the experiment. The findings intimate the application of the microbatch method to space flight and the potential to drastically increase the output of microgravity crystallization research .

Chlamydia protein Pgp3 studied at high resolution in a new crystal form.

Pgp3, a protein implicated in the sexually transmitted disease chlamydia, is described in a new crystal structure. It comprises a three-domain multi-macromolecular complex with two misaligned threefold axes; this comprised a unique challenge that has not been encountered before. A specific intermolecular interaction, possibly of functional significance in receptor binding in chlamydia, might allow the design of a new chemotherapeutic agent against chlamydia.

Enhancing the success of crystallization: strategies and techniques

The talk will present strategies for increasing the chances of success and highlight practical methods that have led to successful crystallization when standard techniques had failed. These methods involve active control of the crystallization environment which has resulted in obtaining crystal hits during screening, as well as producing high quality crystals at the optimisation stage [e.g. 1-3]. A new approach of designing smart materials for automated high-throughput crystallization experiments http://www.imperialinnovations.co.uk/CRMIP will also be presented. Several of the techniques have been patented and commercialised. [1] Khurshid, S. et al. (2014) Nature Protocols, 9, 1621–1633. [2] Khurshid, S. et al. (2015) Acta Crystallographica D 71, 534-540 [3] Nanev, C.N. et al. (2017) Scientific Reports – Nature 7:35821 | DOI: 10.1038/srep35821