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Qin X, Ji J, Chakraborty S, Nangia S. Extending the PARCH Scale: Assessing Hydropathy of Proteins across Multiple Water Models. J Chem Inf Model 2025; 65:2999-3009. [PMID: 40038074 PMCID: PMC11938274 DOI: 10.1021/acs.jcim.4c02415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 02/18/2025] [Accepted: 02/21/2025] [Indexed: 03/06/2025]
Abstract
Quantitative assessment of amino acid hydropathy can be done using the protocol for assigning a residue's character on a hydropathy (PARCH) scale, which assigns values from 0 to 10, with lower values indicating greater hydrophobicity. The merit of the PARCH scale lies in its ability to integrate both the nanoscale topographical features and the chemical properties of amino acid residues when determining hydropathy. In its initial application, we employed the TIP3P water model, optimized for CHARMM36m proteins, to simulate the water behavior around the protein surface. Due to the growing use of the PARCH scale, we have extended its application to three additional all-atom water models: TIP4P, TIP4P-Ew, and TIP5P. Our findings reveal that although PARCH values vary across these water models, the relative hydropathy trends remain consistent. All models successfully distinguished hydrophobic from hydrophilic regions in nanoscale topography, although charged residues showed greater sensitivity to model choice, leading to more significant value variances. Additionally, we evaluated the influence of two other parameters─the force constant used to constrain proteins and the time step of the evaporation process─on the PARCH scale. Overall, the PARCH scale has demonstrated robustness in capturing protein hydropathy across various water models, suggesting its potential applicability with other protein-water force field combinations and even molecular systems beyond proteins.
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Affiliation(s)
- Xuyang Qin
- Department of Biomedical and Chemical
Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Jingjing Ji
- Department of Biomedical and Chemical
Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Somya Chakraborty
- Department of Biomedical and Chemical
Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical and Chemical
Engineering, Syracuse University, Syracuse, New York 13244, United States
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2
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Ji J, Carpentier B, Chakraborty A, Nangia S. An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale. J Chem Theory Comput 2024; 20:1656-1672. [PMID: 37018141 PMCID: PMC10902853 DOI: 10.1021/acs.jctc.3c00106] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Indexed: 04/06/2023]
Abstract
The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.
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Affiliation(s)
- Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Britnie Carpentier
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Arindam Chakraborty
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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3
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Kariev AM, Green ME. Water, Protons, and the Gating of Voltage-Gated Potassium Channels. MEMBRANES 2024; 14:37. [PMID: 38392664 PMCID: PMC10890431 DOI: 10.3390/membranes14020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.
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Affiliation(s)
- Alisher M Kariev
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Michael E Green
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
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4
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Yang L, Guo S, Liao C, Hou C, Jiang S, Li J, Ma X, Shi L, Ye L, He X. Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300022. [PMID: 37483413 PMCID: PMC10362119 DOI: 10.1002/gch2.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Indexed: 07/25/2023]
Abstract
Protein-protein binding enables orderly biological self-organization and is therefore considered a miracle of nature. Protein‒protein binding is driven by electrostatic forces, hydrogen bonding, van der Waals force, and hydrophobic interactions. Among these physical forces, only hydrophobic interactions can be considered long-range intermolecular attractions between proteins due to the electrostatic shielding of surrounding water molecules. Low-entropy hydration shells around proteins drive hydrophobic attraction among them that essentially coordinate protein‒protein binding. Here, an innovative method is developed for identifying low-entropy regions of hydration shells of proteins by screening off pseudohydrophilic groups on protein surfaces and revealing that large low-entropy regions of the hydration shells typically cover the binding sites of individual proteins. According to an analysis of determined protein complex structures, shape matching between a large low-entropy hydration shell region of a protein and that of its partner at the binding sites is revealed as a universal law. Protein‒protein binding is thus found to be mainly guided by hydrophobic collapse between the shape-matched low-entropy hydration shells that is verified by bioinformatics analyses of hundreds of structures of protein complexes, which cover four test systems. A simple algorithm is proposed to accurately predict protein binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- School of AerospaceMechanical and Mechatronic EngineeringThe University of SydneyNSW2006Australia
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chenchen Liao
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chengyu Hou
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Lin Ye
- School of System Design and Intelligent ManufacturingSouthern University of Science and TechnologyShenzhen518055P. R. China
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- Shenzhen STRONG Advanced Materials Research Institute Co., LtdShenzhen518035P. R. China
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5
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Niu Z, Hasegawa K, Deng Y, Zhang Z, Rafailovich M, Simon M, Zhang P. Modeling of the thermal properties of SARS-CoV-2 S-protein. Front Mol Biosci 2022; 9:953064. [PMID: 36237574 PMCID: PMC9550926 DOI: 10.3389/fmolb.2022.953064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
We calculate the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at seven temperatures ranging from 3°C to 95°C by all-atom molecular dynamics (MD) µs-scale simulations with the objectives to understand the structural variations on the temperatures and to determine the potential phase transition while trying to correlate such findings of the S-protein with the observed properties of the SARS-CoV2. Our simulations revealed the following thermal properties of the S-protein: 1) It is structurally stable at 3°C, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; 2) Its structure varies more significantly at temperature values of 60°C-80°C; 3) The sharpest structural variations occur near 60°C, signaling a plausible critical temperature nearby; 4) The maximum deviation of the receptor-binding domain at 37°C, corroborating the anecdotal observations that the virus is most infective at 37°C; 5) The in silico data agree with reported experiments of the SARS-CoV-2 survival times from weeks to seconds by our clustering approach analysis. Our MD simulations at µs scales demonstrated the S-protein's thermodynamics of the critical states at around 60°C, and the stable and denatured states for temperatures below and above this value, respectively.
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Affiliation(s)
- Ziyuan Niu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Karin Hasegawa
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Yuefan Deng
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
- Mathematics, Division of Science, New York University, Abu Dhabi, United Arab Emirates
| | - Ziji Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Miriam Rafailovich
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Marcia Simon
- Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, NY, United States
| | - Peng Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
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6
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Artificial Intelligence in Medicine: Biochemical 3D Modeling and Drug Discovery. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Yang L, Li J, Guo S, Hou C, Liao C, Shi L, Ma X, Jiang S, Zheng B, Fang Y, Ye L, He X. SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. Int J Mol Sci 2021; 22:12114. [PMID: 34829998 PMCID: PMC8619214 DOI: 10.3390/ijms222212114] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of "variants of concern", probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD's binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the "urgent challenge" in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy-enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein-protein complexes is proposed based on the entropy-enthalpy compensation rule. All known structures of RBD-antibody complexes and the RBD-ACE2 complex comply with the entropy-enthalpy compensation rule in providing the driving force behind the spontaneous protein-protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation's reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy-enthalpy compensations between antibodies and the virus at the binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education) and School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Yi Fang
- Mathematical Science Institute, The Australian National University, Canberra, ACT 0200, Australia;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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8
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Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. Int J Mol Sci 2021; 22:9653. [PMID: 34502559 PMCID: PMC8431812 DOI: 10.3390/ijms22179653] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.
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Affiliation(s)
- Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Hongchi Zhang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education), School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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9
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Identifying hydrophobic protein patches to inform protein interaction interfaces. Proc Natl Acad Sci U S A 2021; 118:2018234118. [PMID: 33526682 DOI: 10.1073/pnas.2018234118] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.
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10
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Li Z, Chen Z, Hu J, Li H, Tian SX. A new experimental method for investigations on microstructure of liquid-vapor interface. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2101002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Ziyuan Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ziwei Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jie Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Hao Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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11
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Dybowski R. Artificial Intelligence in Medicine: Biochemical 3D Modeling and Drug Discovery. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_318-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Chen Z, Fu CF, Li Z, Hu J, Li H, Yang J, Tian SX. Identifying the Molecular Orientation and Clusters in the Liquid-Vapor Interface of 1-Propanol by Time-Delayed Mass Spectrometry. J Phys Chem Lett 2020; 11:7510-7516. [PMID: 32813525 DOI: 10.1021/acs.jpclett.0c02097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Structural inhomogeneity of the liquid-vapor interface, such as the spatial orientation of molecular specific groups and the non-uniform distribution of hydrogen-bonded (HB) clusters, is crucial for understanding the physicochemical processes therein. Although the molecular orientation at the outermost layer was authenticated, to date, direct experimental evidence of the in situ existence of different-sized HB clusters, as a long-standing theoretical argument, is still lacking. Here we report time-delayed electron-impact tandem mass spectrometry, and its powerful ability to identify the local structures of the liquid-vapor interface of 1-propanol is demonstrated not only by mapping the molecular orientations both in the outermost layer and in the subsurface but also by validating the existence of the HB molecular dimers in the subsurface by detecting their protonated ions. We further distinguish two different sources of the protonated dimer: the gas-phase protonation of the neutral dimer that evaporates in advance and the time-lag evaporation of the protonated dimer produced in the subsurface. This methodology is a brand-new way to explore the microstructures and the electron-driven chemical reactions in different local regions of the liquid-vapor interface.
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13
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Bagchi A. Latest trends in structure based drug design with protein targets. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:1-23. [PMID: 32312418 DOI: 10.1016/bs.apcsb.2019.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to determine their binding efficacies with protein target. However, the entire process is very lengthy and above all highly expensive. With the advent of supercomputers and increasing computational powers, the search process for finding suitable ligand molecules against target proteins have become more streamlined and cost-effective. Now the entire ligand search process is performed in-silico with the help of the techniques of virtual screening, molecular docking simulations and molecular dynamics studies. In the present chapter, a brief overview of the computational techniques involved in structure based drug designing is presented with a special emphasis on the thermodynamic principles behind the molecular interactions.
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Affiliation(s)
- Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India
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14
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Karasev V. A model of molecular vector machine of proteins. Biosystems 2019; 180:7-18. [PMID: 30878497 DOI: 10.1016/j.biosystems.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/15/2019] [Accepted: 02/02/2019] [Indexed: 01/10/2023]
Abstract
Based on the analysis of NiH⋯Oi-4C bond region of the proteins pentafragments using the quantum chemistry representations, a group of 20 vectors of action has been isolated. These vectors of action are reconstructed by a group of 20 side chains of amino acids being the irreducible representations of vectors. As a result, a model of molecular vector machine of proteins (MVM) has been proposed. This machine includes proteins pentafragments, a system of 20 vectors inside dodecahedron coming out of the Oi-4 atom as from the center and tetrahedral αi-carbon atom with the side chains of amino acids that change as the polypeptide chain grows. A model with the structured canonical set of amino acids based on the principles of antisymmetry was transferred onto the dodecahedron as an MVM element (Karasev et al., 2005; Karasev et al., 2007). The perspective of MVM application for predicting and designing the secondary structure of proteins has been discussed.
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Affiliation(s)
- Vladimir Karasev
- St. Petersburg State Electrotechnical University, Prof. Popov str. 5, 197376, St. Petersburg, Russia.
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15
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Rego NB, Xi E, Patel AJ. Protein Hydration Waters Are Susceptible to Unfavorable Perturbations. J Am Chem Soc 2019; 141:2080-2086. [DOI: 10.1021/jacs.8b11448] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Cui D, Zhang BW, Matubayasi N, Levy RM. The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force. J Chem Theory Comput 2018; 14:512-526. [PMID: 29262255 DOI: 10.1021/acs.jctc.7b01076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Classical density functional theory (DFT) can be used to relate the thermodynamic properties of solutions to the indirect solvent mediated part of the solute-solvent potential of mean force (PMF). Standard, but powerful numerical methods can be used to estimate the solute-solvent PMF from which the indirect part can be extracted. In this work we show how knowledge of the direct and indirect parts of the solute-solvent PMF for water at the interface of a protein receptor can be used to gain insights about how to design tighter binding ligands. As we show, the indirect part of the solute-solvent PMF is equal to the sum of the 1-body (energy + entropy) terms in the inhomogeneous solvation theory (IST) expansion of the solvation free energy. To illustrate the effect of displacing interfacial water molecules with particular direct/indirect PMF signatures on the binding of ligands, we carry out simulations of protein binding with several pairs of congeneric ligands. We show that interfacial water locations that contribute favorably or unfavorably at the 1-body level (energy + entropy) to the solvation free energy of the solute can be targeted as part of the ligand design process. Water locations where the indirect PMF is larger in magnitude provide better targets for displacement when adding a functional group to a ligand core.
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Affiliation(s)
- Di Cui
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Bin W Zhang
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University , Katsura, Kyoto 615-8520, Japan
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
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17
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Barnes R, Sun S, Fichou Y, Dahlquist FW, Heyden M, Han S. Spatially Heterogeneous Surface Water Diffusivity around Structured Protein Surfaces at Equilibrium. J Am Chem Soc 2017; 139:17890-17901. [PMID: 29091442 PMCID: PMC6021025 DOI: 10.1021/jacs.7b08606] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hydration water on the surface of a protein is thought to mediate the thermodynamics of protein-ligand interactions. For hydration water to play a role beyond modulating global protein solubility or stability, the thermodynamic properties of hydration water must reflect on the properties of the heterogeneous protein surface and thus spatially vary over the protein surface. A potent read-out of local variations in thermodynamic properties of hydration water is its equilibrium dynamics spanning picosecond to nanosecond time scales. In this study, we employ Overhauser dynamic nuclear polarization (ODNP) to probe the equilibrium hydration water dynamics at select sites on the surface of Chemotaxis Y (CheY) in dilute solution. ODNP reports on site-specific hydration water dynamics within 5-10 Å of a label tethered to the biomolecular surface on two separate time scales of motion, corresponding to diffusive water (DW) and protein-water coupled motions, referred to as bound water (BW). We find DW dynamics to be highly heterogeneous across the surface of CheY. We identify a significant correlation between DW dynamics and the local hydropathy of the CheY protein surface, empirically determined by molecular dynamics (MD) simulations, and find the more hydrophobic sites to be hydrated with slower diffusing water. Furthermore, we compare the hydration water dynamics on different polypeptides and liposome surfaces and find the DW dynamics on globular proteins to be significantly more heterogeneous than on intrinsically disordered proteins (IDPs), peptides, and liposomes. The heterogeneity in the hydration water dynamics suggests that structured proteins have the capacity to encode information into the surrounding hydration shell.
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Affiliation(s)
- Ryan Barnes
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Sheng Sun
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Yann Fichou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85281, United States
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93106, United States
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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18
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Boschetti E, D'Amato A, Candiano G, Righetti PG. Protein biomarkers for early detection of diseases: The decisive contribution of combinatorial peptide ligand libraries. J Proteomics 2017; 188:1-14. [PMID: 28882677 DOI: 10.1016/j.jprot.2017.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/09/2017] [Accepted: 08/13/2017] [Indexed: 12/31/2022]
Abstract
The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications. Although panels of proteins have been presented, with robust evidence, as potential early-stage biomarkers in these different pathologies, their approval by FDA as novel biomarkers in routine clinical chemistry settings would require plenty of additional work and efforts from the pharma industry. The science environment in universities could simply not afford such heavy monetary investments. SIGNIFICANCE After more than 16years of search for novel biomarkers, to be used in a clinical chemistry set-up, via proteomic analysis (mostly in biological fluids) it was felt a critical review was due. In the present report, though, only papers reporting biomarker discovery via combinatorial peptide ligand libraries are listed and assessed, since this methodology seems to be the most advanced one for digging in depth into low-to very-low-abundance proteins, which might represent important biomarkers for the onset of pathologies. In particular, a large survey has been made for the following diseases, since they appear to have a large incidence on human population and/or represent fatal diseases: ovarian cancer, breast cancer, pancreatic cancer and hepatocellular carcinoma.
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Affiliation(s)
| | - Alfonsina D'Amato
- Quadram Institute of Bioscience, Norwich Research Park, NR4 7UA Norwich, UK
| | - Giovanni Candiano
- Nephrology, Dialysis, Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa, Italy
| | - Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, Milano 20131, Italy.
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19
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Jong K, Grisanti L, Hassanali A. Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β30–35 Chain in Water: A Molecular Dynamics Study. J Chem Inf Model 2017; 57:1548-1562. [DOI: 10.1021/acs.jcim.7b00085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- KwangHyok Jong
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
- Department
of Physics, Kim II Sung University, RyongNam Dong, TaeSong District, Pyongyang, D.P.R., Korea
| | - Luca Grisanti
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
| | - Ali Hassanali
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
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20
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Heldt CL, Zahid A, Vijayaragavan KS, Mi X. Experimental and computational surface hydrophobicity analysis of a non-enveloped virus and proteins. Colloids Surf B Biointerfaces 2017; 153:77-84. [DOI: 10.1016/j.colsurfb.2017.02.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 01/08/2017] [Accepted: 02/09/2017] [Indexed: 12/01/2022]
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21
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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22
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Conformational transition of Aβ 42 inhibited by a mimetic peptide. A molecular modeling study using QM/MM calculations and QTAIM analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Xi E, Remsing RC, Patel AJ. Sparse Sampling of Water Density Fluctuations in Interfacial Environments. J Chem Theory Comput 2016; 12:706-13. [DOI: 10.1021/acs.jctc.5b01037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erte Xi
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Richard C. Remsing
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J. Patel
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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24
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Sui S, Wang X, Zheng H, Guo H, Chen T, Ji DM. Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia. Oncol Lett 2016; 10:3354-3362. [PMID: 26788135 PMCID: PMC4665311 DOI: 10.3892/ol.2015.3761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 07/16/2015] [Indexed: 01/23/2023] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) accounts for over one-quarter of all pediatric cancers. Interacting genes and proteins within the larger human gene interaction network of the human genome are rarely investigated by studies investigating pediatric ALL. In the present study, interaction networks were constructed using the empirical Bayesian approach and the Search Tool for the Retrieval of Interacting Genes/proteins database, based on the differentially-expressed (DE) genes in pediatric ALL, which were identified using the RankProd package. Enrichment analysis of the interaction network was performed using the network-based methods EnrichNet and PathExpand, which were compared with the traditional expression analysis systematic explored (EASE) method. In total, 398 DE genes were identified in pediatric ALL, and LIF was the most significantly DE gene. The co-expression network consisted of 272 nodes, which indicated genes and proteins, and 602 edges, which indicated the number of interactions adjacent to the node. Comparison between EASE and PathExpand revealed that PathExpand detected more pathways or processes that were closely associated with pediatric ALL compared with the EASE method. There were 294 nodes and 1,588 edges in the protein-protein interaction network, with the processes of hematopoietic cell lineage and porphyrin metabolism demonstrating a close association with pediatric ALL. Network enrichment analysis based on the PathExpand algorithm was revealed to be more powerful for the analysis of interaction networks in pediatric ALL compared with the EASE method. LIF and MLLT11 were identified as the most significantly DE genes in pediatric ALL. The process of hematopoietic cell lineage was the pathway most significantly associated with pediatric ALL.
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Affiliation(s)
- Shuxiang Sui
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Xin Wang
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Hua Zheng
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Hua Guo
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Tong Chen
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Dong-Mei Ji
- Department of Pediatrics, Shandong Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
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