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Ladias C, Papakotoulas P, Papaioannou M, Papanikolaou NA. Overcoming phenotypic switching: targeting protein-protein interactions in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1071-1081. [PMID: 38023990 PMCID: PMC10651353 DOI: 10.37349/etat.2023.00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/02/2023] [Indexed: 12/01/2023] Open
Abstract
Alternative protein-protein interactions (PPIs) arising from mutations or post-translational modifications (PTMs), termed phenotypic switching (PS), are critical for the transmission of alternative pathogenic signals and are particularly significant in cancer. In recent years, PPIs have emerged as promising targets for rational drug design, primarily because their high specificity facilitates targeting of disease-related signaling pathways. However, obstacles exist at the molecular level that arise from the properties of the interaction interfaces and the propensity of small molecule drugs to interact with more than one cleft surface. The difficulty in identifying small molecules that act as activators or inhibitors to counteract the biological effects of mutations raises issues that have not been encountered before. For example, small molecules can bind tightly but may not act as drugs or bind to multiple sites (interaction promiscuity). Another reason is the absence of significant clefts on protein surfaces; if a pocket is present, it may be too small, or its geometry may prevent binding. PS, which arises from oncogenic (alternative) signaling, causes drug resistance and forms the basis for the systemic robustness of tumors. In this review, the properties of PPI interfaces relevant to the design and development of targeting drugs are examined. In addition, the interactions between three tyrosine kinase inhibitors (TKIs) employed as drugs are discussed. Finally, potential novel targets of one of these drugs were identified in silico.
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Affiliation(s)
- Christos Ladias
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Epirus, Greece
| | - Pavlos Papakotoulas
- First Department of Clinical Oncology, Theageneio Cancer Hospital, 54639 Thessaloniki, Macedonia, Greece
| | - Maria Papaioannou
- Laboratory of Biological Chemistry, Department of Medicine, Section of Biological Sciences and Preventive Medicine, Aristotle University of Thessaloniki School of Medicine, 54124 Thessaloniki, Macedonia, Greece
| | - Nikolaos A. Papanikolaou
- Laboratory of Biological Chemistry, Department of Medicine, Section of Biological Sciences and Preventive Medicine, Aristotle University of Thessaloniki School of Medicine, 54124 Thessaloniki, Macedonia, Greece
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2
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Colorado-Peralta R, María Rivera-Villanueva J, Manuel Mora-Hernández J, Morales-Morales D, Ángel Alfonso-Herrera L. An overview of the role of supramolecular interactions in gas storage using MOFs. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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3
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Jung W, Sengupta K, Wendel BM, Helmann JD, Chen P. Biphasic unbinding of a metalloregulator from DNA for transcription (de)repression in Live Bacteria. Nucleic Acids Res 2020; 48:2199-2208. [PMID: 32009151 PMCID: PMC7049717 DOI: 10.1093/nar/gkaa056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/06/2020] [Accepted: 01/17/2020] [Indexed: 11/12/2022] Open
Abstract
Microorganisms use zinc-sensing regulators to alter gene expression in response to changes in the availability of zinc, an essential micronutrient. Under zinc-replete conditions, the Fur-family metalloregulator Zur binds to DNA tightly in its metallated repressor form to Zur box operator sites, repressing the transcription of zinc uptake transporters. Derepression comes from unbinding of the regulator, which, under zinc-starvation conditions, exists in its metal-deficient non-repressor forms having no significant affinity with Zur box. While the mechanism of transcription repression by Zur is well-studied, little is known on how derepression by Zur could be facilitated. Using single-molecule/single-cell measurements, we find that in live Escherichia coli cells, Zur's unbinding rate from DNA is sensitive to Zur protein concentration in a first-of-its-kind biphasic manner, initially impeded and then facilitated with increasing Zur concentration. These results challenge conventional models of protein unbinding being unimolecular processes and independent of protein concentration. The facilitated unbinding component likely occurs via a ternary complex formation mechanism. The impeded unbinding component likely results from Zur oligomerization on chromosome involving inter-protein salt-bridges. Unexpectedly, a non-repressor form of Zur is found to bind chromosome tightly, likely at non-consensus sequence sites. These unusual behaviors could provide functional advantages in Zur's facile switching between repression and derepression.
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Affiliation(s)
- Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kushal Sengupta
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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4
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Kim DM, Yao X, Vanam RP, Marlow MS. Measuring the effects of macromolecular crowding on antibody function with biolayer interferometry. MAbs 2019; 11:1319-1330. [PMID: 31401928 PMCID: PMC6748605 DOI: 10.1080/19420862.2019.1647744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biotherapeutic proteins are commonly dosed at high concentrations into the blood, which is an inherently complex, crowded solution with substantial protein content. The effects of macromolecular crowding may lead to an appreciable level of non-specific hetero-association in this physiological environment. Therefore, developing a method to characterize the diverse consequences of non-specific interactions between proteins under such non-ideal, crowded conditions, which deviate substantially from those commonly employed for in vitro characterization, is vital to achieving a more complete picture of antibody function in a biological context. In this study, we investigated non-specific interactions between human serum albumin (HSA) and two monoclonal antibodies (mAbs) by static light scattering and determined these interactions are both ionic strength-dependent and mAb-dependent. Using biolayer interferometry (BLI), we assessed the effect of HSA on antigen binding by mAbs, demonstrating that these non-specific interactions have a functional impact on mAb:antigen interactions, particularly at low ionic strength. While this effect is mitigated at physiological ionic strength, our in vitro data support the notion that HSA in the blood may lead to non-specific interactions with mAbs in vivo, with a potential impact on their interactions with antigen. Furthermore, the BLI method offers a high-throughput advantage compared to orthogonal techniques such as analytical ultracentrifugation and is amenable to a greater variety of solution conditions compared to nuclear magnetic resonance spectroscopy. Our study demonstrates that BLI is a viable technology for examining the impact of non-specific interactions on specific biologically relevant interactions, providing a direct method to assess binding events in crowded conditions.
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Affiliation(s)
- Dorothy M Kim
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Xiao Yao
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Ram P Vanam
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Michael S Marlow
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA.,Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc ., Ridgefield , CT , USA
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5
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Cicaloni V, Trezza A, Pettini F, Spiga O. Applications of in Silico Methods for Design and Development of Drugs Targeting Protein-Protein Interactions. Curr Top Med Chem 2019; 19:534-554. [PMID: 30836920 DOI: 10.2174/1568026619666190304153901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/02/2019] [Accepted: 01/25/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Identification of Protein-Protein Interactions (PPIs) is a major challenge in modern molecular biology and biochemistry research, due to the unquestionable role of proteins in cells, biological process and pathological states. Over the past decade, the PPIs have evolved from being considered a highly challenging field of research to being investigated and examined as targets for pharmacological intervention. OBJECTIVE Comprehension of protein interactions is crucial to known how proteins come together to build signalling pathways, to carry out their functions, or to cause diseases, when deregulated. Multiplicity and great amount of PPIs structures offer a huge number of new and potential targets for the treatment of different diseases. METHODS Computational techniques are becoming predominant in PPIs studies for their effectiveness, flexibility, accuracy and cost. As a matter of fact, there are effective in silico approaches which are able to identify PPIs and PPI site. Such methods for computational target prediction have been developed through molecular descriptors and data-mining procedures. RESULTS In this review, we present different types of interactions between protein-protein and the application of in silico methods for design and development of drugs targeting PPIs. We described computational approaches for the identification of possible targets on protein surface and to detect of stimulator/ inhibitor molecules. CONCLUSION A deeper study of the most recent bioinformatics methodologies for PPIs studies is vital for a better understanding of protein complexes and for discover new potential PPI modulators in therapeutic intervention.
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Affiliation(s)
- Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy.,Toscana Life Sciences Foundation, via Fiorentina 1, 53100 Siena, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Francesco Pettini
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy (Dept. of Excellence 2018-2022), University of Siena, via A. Moro 2, 53100 Siena, Italy
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Copley HC, Elango M, Kosmoliaptsis V. Assessment of human leukocyte antigen immunogenicity: current methods, challenges and opportunities. Curr Opin Organ Transplant 2019; 23:477-485. [PMID: 29870434 PMCID: PMC6082597 DOI: 10.1097/mot.0000000000000544] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Purpose of review Donor–recipient human leukocyte antigen (HLA) matching improves outcomes after solid-organ transplantation, but current assessment of HLA incompatibility is inadequate as it does not consider the relative immunogenicity of individual HLA mismatches. In this article, we review existing strategies for assessing HLA immunogenicity and discuss current challenges and future opportunities in this field. Recent findings Current HLA immunogenicity algorithms focus primarily on the humoral component of the alloimmune response and aim to determine a measure of ‘dissimilarity’ between donor and recipient HLA. This can be achieved by deriving information from comparison of donor and recipient HLA at the amino acid sequence, structural and/or the physicochemical level, accounting for both B-cell and T-cell pathways of alloreactivity. Substantial evidence now supports the superiority of this molecular definition of HLA incompatibility, over conventional enumeration of HLA antigenic differences, for assessing the risk of humoral alloimmunity and for predicting graft outcomes after transplantation. Summary Significant progress has been made in developing computational HLA immunogenicity algorithms that offer exciting opportunities for a more rational approach to determining the degree of donor–recipient HLA incompatibility and to defining HLA-related immunological risk. A number of challenges now need to be overcome to enable their implementation into clinical practice.
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Affiliation(s)
- Hannah C Copley
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital
| | - Madhivanan Elango
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation at the University of Cambridge, Cambridge, UK
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7
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Jin B, Tan W, Zhang C, Wu J, Chen J, Zhang S, Wu P. High-Performance Terahertz Sensing at Exceptional Points in a Bilayer Structure. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Biaobing Jin
- Research Institute of Superconductor Electronics; School of Electronic Science and Engineering; Nanjing University; Nanjing 210023 China
| | - Wei Tan
- Microsystem and Terahertz Research Center; China Academy of Engineering Physics; Chengdu 610200 China
| | - Caihong Zhang
- Research Institute of Superconductor Electronics; School of Electronic Science and Engineering; Nanjing University; Nanjing 210023 China
| | - Jingbo Wu
- Research Institute of Superconductor Electronics; School of Electronic Science and Engineering; Nanjing University; Nanjing 210023 China
| | - Jian Chen
- Research Institute of Superconductor Electronics; School of Electronic Science and Engineering; Nanjing University; Nanjing 210023 China
| | - Shuang Zhang
- School of Physics and Astronomy; University of Birmingham; Birmingham B15 2TT UK
| | - Peiheng Wu
- Research Institute of Superconductor Electronics; School of Electronic Science and Engineering; Nanjing University; Nanjing 210023 China
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8
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Abrikosov AI, Stenqvist B, Lund M. Steering patchy particles using multivalent electrolytes. SOFT MATTER 2017; 13:4591-4597. [PMID: 28593204 DOI: 10.1039/c7sm00470b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Proteins and many recently designed colloids can be regarded as patchy particles where directional interactions strongly influence and govern assembly behavior. Using explicit ion implicit solvent Metropolis Monte Carlo simulations, we investigate spherical model particles, carrying both charge and electric patches, in dilute aqueous 1 : 1, 1 : 3, and 3 : 1 electrolyte solutions. Striking differences in pair interaction free energies and orientational correlations are induced by three different salts which are discussed and rationalized in terms of ion-binding to surface groups, ion-ion correlations, and double layer forces. These findings suggest a general strategy where directional, intermolecular interactions can be invoked and tuned via small amounts of a carefully chosen electrolyte.
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Affiliation(s)
- Alexei I Abrikosov
- Division of Physical Chemistry, Lund University, POB 124, SE-22100 Lund, Sweden.
| | - Björn Stenqvist
- Division of Theoretical Chemistry, Lund University, POB 124, SE-22100 Lund, Sweden.
| | - Mikael Lund
- Division of Theoretical Chemistry, Lund University, POB 124, SE-22100 Lund, Sweden.
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9
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Lund M. Anisotropic protein-protein interactions due to ion binding. Colloids Surf B Biointerfaces 2015; 137:17-21. [PMID: 26162300 DOI: 10.1016/j.colsurfb.2015.05.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 10/23/2022]
Abstract
Self-association of proteins is strongly affected by long-range electrostatic interactions caused by equilibrium adsorption of small ions such as protons and multivalent metals. By affecting the molecular net charge, solution pH is thus a widely used parameter to tune stability and phase behavior of proteins. We here review recent studies where the charge distribution is perturbed not only by protons, but also by other binding ions, leading to a rich and inherently anisotropic charge distribution. Focus is on coarse grained simulation techniques, coupled to experiments of protein-protein interaction at varying salt and pH conditions. Finally, and with future bio-colloidal models in mind, we discuss the validity of coarse graining charge anisotropy using electric multipoles.
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Affiliation(s)
- Mikael Lund
- Division of Theoretical Chemistry, Lund University, PO Box 124, SE-22100 Lund, Sweden.
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10
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Kurut A, Dicko C, Lund M. Dimerization of Terminal Domains in Spiders Silk Proteins Is Controlled by Electrostatic Anisotropy and Modulated by Hydrophobic Patches. ACS Biomater Sci Eng 2015; 1:363-371. [DOI: 10.1021/ab500039q] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Anıl Kurut
- Division of Theoretical Chemistry,
Chemical Center,
and ‡Division of Pure
and Applied Biochemistry, Chemical Center, Lund University, SE-22100 Lund, Sweden
| | - Cedric Dicko
- Division of Theoretical Chemistry,
Chemical Center,
and ‡Division of Pure
and Applied Biochemistry, Chemical Center, Lund University, SE-22100 Lund, Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry,
Chemical Center,
and ‡Division of Pure
and Applied Biochemistry, Chemical Center, Lund University, SE-22100 Lund, Sweden
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11
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Schröder C, Steinhauser O, Sasisanker P, Weingärtner H. Orientational alignment of amyloidogenic proteins in pre-aggregated solutions. PHYSICAL REVIEW LETTERS 2015; 114:128101. [PMID: 25860772 DOI: 10.1103/physrevlett.114.128101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 06/04/2023]
Abstract
In the present study we combine dielectric relaxation spectroscopy with generalized Born simulations to explore the role of orientational order for protein aggregation in solutions of bovine pancreatic insulin at various pH conditions. Under aggregation-prone conditions at low pH, insulin monomers prefer antiparallel dipole alignments, which are consistent with the orientation of the monomeric subunits in the dimer structure. This alignment is also true for two dimers, suggesting that already at moderate protein concentrations the species assemble in equilibrium clusters, in which the molecules adopt preferred orientations also found for the protomers of the corresponding oligomers.
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Affiliation(s)
- C Schröder
- Department of Computational Biological Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
| | - O Steinhauser
- Department of Computational Biological Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
| | - P Sasisanker
- Department of Physical Chemistry II, Ruhr-University of Bochum, Germany and Praj Matrix The Innovation Center Urawade, Pune 412108, India
| | - H Weingärtner
- Department of Physical Chemistry II, Ruhr-University of Bochum, Building NC 6-25, 44780 Bochum, Germany
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12
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Structural and electrostatic analysis of HLA B-cell epitopes: inference on immunogenicity and prediction of humoral alloresponses. Curr Opin Organ Transplant 2015; 19:420-7. [PMID: 24977436 DOI: 10.1097/mot.0000000000000108] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
PURPOSE OF REVIEW The immunogenic capacity of donor human leukocyte antigen (HLA) to induce humoral immune responses is not an intrinsic property of the mismatched alloantigen but depends on the HLA phenotype of the recipient. In recent years, advances in molecular sequence technology and information from X-ray crystallography have enabled structural comparison of donor and recipient HLA type providing an opportunity for a more rational approach for determining HLA compatibility. In this article, we review studies investigating the molecular basis of antibody-antigen interactions and present computational approaches to determine the complex physiochemical and structural properties of B-cell epitopes. RECENT FINDINGS The relative immunogenicity of individual HLA mismatches may be predicted from analysis of polymorphic amino acids at continuous and discontinuous HLA sequence positions. The use of alloantigen sequence information alone, however, provides limited insight into key determinants of B-cell epitope immunogenicity, such as the orientation, accessibility and physiochemical properties of amino acid side chains. Advances in computational molecular modelling techniques now enable assessment of HLA-alloantibody interactions at the atomic level. Recent evidence supports a strong link between HLA B-cell epitope surface electrostatic potential and their immunogenicity. SUMMARY Assessment of the surface electrostatic properties of HLA alloantigens and computational analyses of HLA-alloantibody interactions represent a promising area for future research into the molecular basis of HLA immunogenicity and antigenicity.
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13
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Kaieda S, Lund M, Plivelic TS, Halle B. Weak self-interactions of globular proteins studied by small-angle X-ray scattering and structure-based modeling. J Phys Chem B 2014; 118:10111-9. [PMID: 25117055 DOI: 10.1021/jp505809v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty acid-binding protein (IFABP) is determined from SAXS measurements at multiple concentrations, from Monte Carlo simulations with a coarse-grained structure-based interaction model, and from analytic approximate solutions of two idealized colloidal interaction models without adjustable parameters. By combining these approaches, we find that the structure factor is essentially determined by hard-core and screened electrostatic interactions. Other soft short-ranged interactions (van der Waals and solvation-related) are either individually insignificant or tend to cancel out. The structure factor is also not significantly affected by charge fluctuations. For Mb and IFABP, with a small net charge and relatively symmetric charge distribution, the structure factor is well described by a hard-sphere model. For BPTI, with a larger net charge, screened electrostatic repulsion is also important, but the asymmetry of the charge distribution reduces the repulsion from that predicted by a charged hard-sphere model with the same net charge. Such charge asymmetry may also amplify the effect of shape asymmetry on the protein-protein potential of mean force.
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Affiliation(s)
- Shuji Kaieda
- Department of Biophysical Chemistry, Lund University , P.O. Box 124, SE-22100 Lund, Sweden
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14
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Roberts D, Keeling R, Tracka M, van der Walle CF, Uddin S, Warwicker J, Curtis R. The role of electrostatics in protein-protein interactions of a monoclonal antibody. Mol Pharm 2014; 11:2475-89. [PMID: 24892385 DOI: 10.1021/mp5002334] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Understanding how protein-protein interactions depend on the choice of buffer, salt, ionic strength, and pH is needed to have better control over protein solution behavior. Here, we have characterized the pH and ionic strength dependence of protein-protein interactions in terms of an interaction parameter kD obtained from dynamic light scattering and the osmotic second virial coefficient B22 measured by static light scattering. A simplified protein-protein interaction model based on a Baxter adhesive potential and an electric double layer force is used to separate out the contributions of longer-ranged electrostatic interactions from short-ranged attractive forces. The ionic strength dependence of protein-protein interactions for solutions at pH 6.5 and below can be accurately captured using a Deryaguin-Landau-Verwey-Overbeek (DLVO) potential to describe the double layer forces. In solutions at pH 9, attractive electrostatics occur over the ionic strength range of 5-275 mM. At intermediate pH values (7.25 to 8.5), there is a crossover effect characterized by a nonmonotonic ionic strength dependence of protein-protein interactions, which can be rationalized by the competing effects of long-ranged repulsive double layer forces at low ionic strength and a shorter ranged electrostatic attraction, which dominates above a critical ionic strength. The change of interactions from repulsive to attractive indicates a concomitant change in the angular dependence of protein-protein interaction from isotropic to anisotropic. In the second part of the paper, we show how the Baxter adhesive potential can be used to predict values of kD from fitting to B22 measurements, thus providing a molecular basis for the linear correlation between the two protein-protein interaction parameters.
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Affiliation(s)
- D Roberts
- School of Chemical Engineering and Analytical Science, The University of Manchester , Sackville Street, Manchester M13 9PL, U.K
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15
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Semyonov SA. A study of electrolytic coagulation of gold sols by the method of localized surface plasmon resonance spectroscopy. COLLOID JOURNAL 2013. [DOI: 10.1134/s1061933x13040091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Scherer TM. Cosolute Effects on the Chemical Potential and Interactions of an IgG1 Monoclonal Antibody at High Concentrations. J Phys Chem B 2013; 117:2254-66. [DOI: 10.1021/jp3091717] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas M. Scherer
- Genentech (a Member of the
Roche Group), Late Stage Pharmaceutical Development, 1 DNA Way, South
San Francisco, California 94080, United States
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17
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Molecular dynamics simulation of the interaction between protein tyrosine phosphatase 1B and aryl diketoacid derivatives. J Mol Graph Model 2012; 38:186-93. [PMID: 23085163 DOI: 10.1016/j.jmgm.2012.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/28/2012] [Accepted: 06/28/2012] [Indexed: 11/22/2022]
Abstract
The protein tyrosine phosphatase 1B (PTP-1B) is acknowledged as an outstanding therapeutic target for the treatment of diabetes, obesity and cancer. In this work, six aryl diketoacid compounds have been studied on the basis of molecular dynamics simulations. Hydrogen bonds, binding energies and conformation changes of the WPD loop have been analyzed. The results indicated that their activation model falls into two parts: the target region of the monomeric aryl diketoacid compounds is the active site, whereas the target region of the dimeric aryl diketoacid compounds is the WPD loop or the R loop. The van der Waals interactions exhibit stronger effects than the short-range electrostatic interactions. The van der Waals interaction energy and the IC50 values exhibit an approximately exponential relationship. Furthermore, the van der Waals interactions cooperate with the hydrogen bond interactions. This study provides a more thorough understanding of the PTP-1B inhibitor binding processes.
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Kiraga-Motoszko K, Niedzwiecka A, Modrak-Wojcik A, Stepinski J, Darzynkiewicz E, Stolarski R. Thermodynamics of molecular recognition of mRNA 5' cap by yeast eukaryotic initiation factor 4E. J Phys Chem B 2011; 115:8746-54. [PMID: 21650456 DOI: 10.1021/jp2012039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanisms underlying the recognition of the mRNA 5' terminal structure called "cap" by the eukaryotic initiation factor 4E (eIF4E) are crucial for cap-dependent translation. To gain a deeper insight into how the yeast eIF4E interacts with the cap structure, isothermal titration calorimetry and the van't Hoff analysis based on intrinsic protein fluorescence quenching upon titration with a series of chemical cap analogs were performed, providing a consistent thermodynamic description of the binding process in solution. Equilibrium association constants together with thermodynamic parameters revealed similarities and differences between yeast and mammalian eIF4Es. The yeast eIF4E complex formation was enthalpy-driven and entropy-opposed for each cap analog at 293 K. A nontrivial isothermal enthalpy–entropy compensation was found, described by a compensation temperature, T(c) = 411 ± 18 K. For a low affinity analog, 7-methylguanosine monophosphate, a heat capacity change was detected, ΔC(p)° = +5.2 ± 1.3 kJ·mol(-1)·K(-1). The charge-related interactions involving the 5′-5′ triphosphate bridge of the cap and basic amino acid side chains at the yeast eIF4E cap-binding site were significantly weaker (by ΔΔH°(vH) of about +10 kJ·mol(-1)) than those for the mammalian homologues, suggesting their optimization during the evolution.
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Affiliation(s)
- Katarzyna Kiraga-Motoszko
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
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Abstract
The role of electrostatics in protein-protein interactions and binding is reviewed in this paper. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and the basic electrostatic effects occurring upon the formation of the complex are discussed. The effect of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated which indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartments. The similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity.
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Affiliation(s)
- Zhe Zhang
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson,SC 29634, USA
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Pichierri F. The electronic structure and dipole moment of charybdotoxin, a scorpion venom peptide with K+ channel blocking activity. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Persson BA, Lund M. Association and electrostatic steering of alpha-lactalbumin-lysozyme heterodimers. Phys Chem Chem Phys 2009; 11:8879-85. [PMID: 20449034 DOI: 10.1039/b909179c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The salt and pH dependent association of hen egg white lysozyme with alpha-lactalbumin whey proteins has been studied using molecular level Monte Carlo simulations. A highly uneven charge distribution of alpha-lactalbumin leads to strongly ordered heterodimers that may facilitate the formation of structured, mesoscopic aggregates. This electrostatic steering gives rise to 80% alignment at 5 mM 1 : 1 salt which, due to screening, diminishes to 60% at 100 mM salt. The free energy of interaction minima, dominated by electrostatics, ranges between -9 kT at 1 mM salt to -2 kT at 100 mM (neutral pH). Calculated osmotic second virial cross coefficients indicate complexation in the pH interval 6-10. Multivalent ions are found to effectively destabilize the protein complex and, at constant ionic strength, the order is La(3+) > Ca(2+) > Mg(2+) > Na(+). Upon binding of calcium to alpha-lactalbumin both the interaction and orientational alignment with lysozyme are reduced due to induced changes in the whey protein charge distribution. This potentially explains the experimentally observed absence of supramolecular structuring for the calcium loaded holo alpha-lactalbumin. Where available, good agreement is found with experimental data.
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Affiliation(s)
- Björn A Persson
- Department of Theoretical Chemistry, Chemical Center, POB 124, S-221 00 Lund, Sweden
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