Publications
73 results found
Saridakis E, Vishwakarma R, Lai-Kee-Him J, et al., 2022, Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism, COMMUNICATIONS BIOLOGY, Vol: 5
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- Citations: 1
Panagiotakis S, Saridakis E, Malanga M, et al., 2021, A Self-locked beta-Cyclodextrin-rhodamine B Spirolactam with Photoswitching Properties, CHEMISTRY-AN ASIAN JOURNAL, Vol: 17, ISSN: 1861-4728
Saridakis E, 2021, The genetic informational network: how DNA conveys semantic information, HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES, Vol: 43, ISSN: 0391-9714
Govada L, Saridakis E, Kassen SC, et al., 2021, X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5, IUCrJ, Vol: 8, Pages: 678-683, ISSN: 2052-2525
C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.
Saridakis E, Coste F, 2021, Thermal Shift Assay for Characterizing the Stability of RNA Helicases and Their Interaction with Ligands, RNA REMODELING PROTEINS, 2 EDITION, Vol: 2209, Pages: 73-85, ISSN: 1064-3745
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- Citations: 1
Mpakali A, Saridakis E, Giastas P, et al., 2020, Structural Basis of Inhibition of Insulin-Regulated Aminopeptidase by a Macrocyclic Peptidic Inhibitor, ACS MEDICINAL CHEMISTRY LETTERS, Vol: 11, Pages: 1429-1434, ISSN: 1948-5875
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- Citations: 10
Stelzl LS, Mavridou DA, Saridakis E, et al., 2020, Local frustration determines loop opening during the catalytic cycle of an oxidoreductase., eLife, Vol: 9, Pages: 1-27, ISSN: 2050-084X
Local structural frustration, the existence of mutually exclusive competing interactions, may explain why some proteins are dynamic while others are rigid. Frustration is thought to underpin biomolecular recognition and the flexibility of protein-binding sites. Here, we show how a small chemical modification, the oxidation of two cysteine thiols to a disulfide bond, during the catalytic cycle of the N-terminal domain of the key bacterial oxidoreductase DsbD (nDsbD), introduces frustration ultimately influencing protein function. In oxidized nDsbD, local frustration disrupts the packing of the protective cap-loop region against the active site allowing loop opening. By contrast, in reduced nDsbD the cap loop is rigid, always protecting the active-site thiols from the oxidizing environment of the periplasm. Our results point toward an intricate coupling between the dynamics of the active-site cysteines and of the cap loop which modulates the association reactions of nDsbD with its partners resulting in optimized protein function.
Nanev C, Saridakis E, Govada L, et al., 2019, Hydrophobic Interface-assisted protein crystallization: theory and experiment, ACS Applied Materials and Interfaces, Vol: 11, Pages: 12931-12940, ISSN: 1944-8244
Macromolecular crystallization is crucially important to a large number of scientific fields, including structural biology, drug design, formulation and delivery, the manufacture of biomaterials, and the preparation of foodstuffs. The purpose of this study is to facilitate control of crystallization, by investigating hydrophobic interface-assisted protein crystallization both theoretically and experimentally. The application of hydrophobic liquids as nucleation promoters or suppressors has rarely been investigated, and provides an underused avenue to explore in protein crystallization. Theoretically, crystal nucleation is regarded as a two-step process, the first step being a local increase in protein concentration due to its adsorption on the hydrophobic surface. Subsequently, the protein is ordered in a crystal lattice. The energetic aspect of crystal nucleation on water/hydrophobic substance interfaces is approached by calculating the balance between the cohesive energy maintaining integrity of the 2D-crystal nucleus and the sum of destructive energies tending to tear up the crystal. This is achieved by comparing the number of bonds shared by the units forming the crystal and the number of unshared (dangling) bonds on the crystal surface pointing toward the solution. The same approach is extended to 3D protein crystal nucleation at water/hydrophobic liquid interfaces. Experimentally, we studied protein crystalliza-tion over oils and other hydrophobic liquids (paraffin oil, FC-70 Fluorinert fluorinated oil, and three chlorinated hydrocarbons). Crystallization of α-lactalbumin and lysozyme are compared, and additional information is acquired by studying α-crustacyanin, trypsin, an insulin analogue and protein Lpg2936. Depending on the protein type, concentration, and the interface aging time, the proteins exhibit different crystallization propensities depending on the hydrophobic liquid used. Some hydrophobic liquids provoke an increase in the effective
Saridakis E, 2019, PROTEIN THERMODYNAMIC PARAMETERS TO UNDERSTAND AND GUIDE CRYSTALLISATION, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: E48-E48, ISSN: 2053-2733
Mpakali A, Saridakis E, Harlos K, et al., 2017, Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 60, Pages: 2963-2972, ISSN: 0022-2623
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- Citations: 28
Mpakali A, Giastas P, Deprez-Poulain R, et al., 2017, Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency, ACS MEDICINAL CHEMISTRY LETTERS, Vol: 8, Pages: 333-337, ISSN: 1948-5875
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- Citations: 15
Nanev CN, Saridakis E, Chayen N, 2017, Protein crystal nucleation in pores, Scientific Reports, Vol: 7, ISSN: 2045-2322
The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials.
Govada L, Saridakis E, Khurshid S, et al., 2017, Enhancing the success of crystallization: strategies and techniques, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: C1082-C1082, ISSN: 2053-2733
Govada L, Saridakis E, Kassen S, et al., 2017, Smart materials for increasing the success of protein crystallization, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: C1138-C1138, ISSN: 2053-2733
Stavros P, Saridakis E, Nounesis G, 2016, Influence of Precipitating Agents on Thermodynamic Parameters of Protein Crystallization Solutions, BIOPOLYMERS, Vol: 105, Pages: 642-652, ISSN: 0006-3525
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- Citations: 2
Leese HS, Govada L, Saridakis E, et al., 2016, Reductively PEGylated carbon nanomaterials andtheir use to nucleate 3D protein crystals:a comparison of dimensionality, Chemical Science, Vol: 7, Pages: 2916-2923, ISSN: 2041-6539
A range of carbon nanomaterials, with varying dimensionality, were dispersed by a non-damaging and versatile chemical reduction route, and subsequently grafted by reaction with methoxy polyethylene glycol (mPEG) monobromides. The use of carbon nanomaterials with different geometries provides both a systematic comparison of surface modification chemistry and the opportunity to study factors affecting specific applications. Multi-walled carbon nanotubes, single-walled carbon nanotubes, graphite nanoplatelets, exfoliated few layer graphite and carbon black were functionalized with mPEG-Br, yielding grafting ratios relative to the nanocarbon framework between ca. 7 and 135 wt%; the products were characterised by Raman spectroscopy, TGA-MS, and electron microscopy. The functionalized materials were tested as nucleants by subjecting them to rigorous protein crystallization studies. Sparsely functionalized flat sheet geometries proved exceptionally effective at inducing crystallization of six proteins. This new class of nucleant, based on PEG grafted graphene-related materials, can be widely applied to promote the growth of 3D crystals suitable for X-ray crystallography. The association of the protein ferritin with functionalized exfoliated few layer graphite was directly visualized by transmission electron microscopy, illustrating the formation of ordered clusters of protein molecules critical to successful nucleation.
Saridakis E, 2016, Information, Reality, and Modern Physics, INTERNATIONAL STUDIES IN THE PHILOSOPHY OF SCIENCE, Vol: 30, Pages: 327-341, ISSN: 0269-8595
Mpakali A, Giastas P, Mathioudakis N, et al., 2015, Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 290, Pages: 26021-26032
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- Citations: 55
Mpakali A, Saridakis E, Harlos K, et al., 2015, Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing, JOURNAL OF IMMUNOLOGY, Vol: 195, Pages: 2842-2851, ISSN: 0022-1767
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- Citations: 32
Chain B, Arnold J, Akthar S, et al., 2015, A Linear Epitope in the N-Terminal Domain of CCR5 and Its Interaction with Antibody., PLOS One, Vol: 10, ISSN: 1932-6203
The CCR5 receptor plays a role in several key physiological and pathological processes and is an important therapeutic target. Inhibition of the CCR5 axis by passive or active immunisation offers one very selective strategy for intervention. In this study we define a new linear epitope within the extracellular domain of CCR5 recognised by two independently produced monoclonal antibodies. A short peptide encoding the linear epitope can induce antibodies which recognise the intact receptor when administered colinear with a tetanus toxoid helper T cell epitope. The monoclonal antibody RoAb 13 is shown to bind to both cells and peptide with moderate to high affinity (6x10^8 and 1.2x107 M-1 respectively), and binding to the peptide is enhanced by sulfation of tyrosines at positions 10 and 14. RoAb13, which has previously been shown to block HIV infection, also blocks migration of monocytes in response to CCR5 binding chemokines and to inflammatory macrophage conditioned medium. A Fab fragment of RoAb13 has been crystallised and a structure of the antibody is reported to 2.1 angstrom resolution.
Zervoudi E, Saridakis E, Birtley J, et al., 2014, Development of potent pseudopeptide phosphinic inhibitors of antigen-trimming aminopeptidases that can enhance cytotoxic t-cell responses against cancer cells, FEBS EMBO 2014 Conference, Publisher: WILEY-BLACKWELL, Pages: 114-114, ISSN: 1742-464X
Mathioudakis N, Zervoudi E, Saridakis E, et al., 2014, Crystal structure of human aminopeptidase ERAP2 in the absence of catalytic Zn(II) atom, FEBS EMBO 2014 Conference, Publisher: WILEY-BLACKWELL, Pages: 110-110, ISSN: 1742-464X
Khurshid S, Saridakis E, Govada L, et al., 2014, Porous nucleating agents for protein crystallization, Nature Protocols, Vol: 9, Pages: 1621-1633, ISSN: 1750-2799
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.
Mavridou DAI, Saridakis E, Kritsiligkou P, et al., 2014, An Extended Active-site Motif Controls the Reactivity of the Thioredoxin Fold, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 289, Pages: 8681-8696
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- Citations: 6
Govada L, Saridakis E, Khurshid S, et al., 2014, Enhancing the success of crystallization: strategies and techniques, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: C1082-C1082, ISSN: 2053-2733
Govada L, Saridakis E, Kassen S, et al., 2014, Smart materials for increasing the success of protein crystallization, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: C1138-C1138, ISSN: 2053-2733
Zervoudi E, Saridakis E, Birtley JR, et al., 2013, Rationally designed inhibitor targeting antigen-trimming aminopeptidases enhances antigen presentation and cytotoxic T-cell responses, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 19890-19895, ISSN: 0027-8424
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- Citations: 97
Saridakis E, Chayen NE, 2013, Imprinted polymers assisting protein crystallization, TRENDS IN BIOTECHNOLOGY, Vol: 31, Pages: 515-520, ISSN: 0167-7799
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- Citations: 37
Evnouchidou I, Birtley J, Seregin S, et al., 2012, A common polymorphism in ER aminopeptidase 2 induces a specificity switch that leads to altered processing of antigenic peptides, Publisher: WILEY-BLACKWELL, Pages: S42-S42, ISSN: 1075-2617
Evnouchidou I, Birtley J, Seregin S, et al., 2012, A Common Single Nucleotide Polymorphism in Endoplasmic Reticulum Aminopeptidase 2 Induces a Specificity Switch That Leads to Altered Antigen Processing, JOURNAL OF IMMUNOLOGY, Vol: 189, Pages: 2383-2392, ISSN: 0022-1767
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- Citations: 76
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