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Nochebuena J, Piquemal JP, Liu S, Cisneros GA. Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields. J Chem Theory Comput 2023; 19:7715-7730. [PMID: 37888874 DOI: 10.1021/acs.jctc.3c00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Understanding cooperativity and frustration is crucial for studying biological processes such as molecular recognition and protein aggregation. Force fields have been extensively utilized to explore cooperativity in the formation of protein secondary structures and self-assembled systems. Multiple studies have demonstrated that polarizable force fields provide more accurate descriptions of this phenomenon compared to fixed-charge pairwise nonpolarizable force fields, thanks to the incorporation of polarization effects. In this study, we assess the performance of the AMOEBA polarizable force field and the AMBER and OPLS nonpolarizable pairwise force fields in capturing positive and negative cooperativity recently explored in neutral and charged molecular clusters using density functional theory. Our findings show that polarizable and nonpolarizable force fields qualitatively reproduce the relative cooperativity observed in electron structure calculations. However, AMBER and OPLS fail to describe absolute cooperativity. In contrast, AMOEBA accounts for the absolute cooperativity by considering interactions beyond pairwise interactions. According to the energy decomposition analysis, it is observed that the electrostatic interactions calculated with the AMBER and OPLS force fields seem to play an important and counterintuitive role in reproducing the adiabatic interaction energies calculated with density functional theory. However, it is important to note that these force fields, due to their nature, do not explicitly incorporate many-body effects, which limits their ability to accurately describe cooperativity. On the other hand, frustration in polarizable and nonpolarizable force fields is caused by changes in bond stretching and angle bending terms of the building blocks when they are forming a complex.
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Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie théorique, Sorbonne Université, UMR 7616 CNRS, Paris 75005, France
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
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Muñoz-Gutiérrez C, Adasme-Carreño F, Alzate-Morales J, Ireta J. Effect of strand register in the stability and reactivity of crystals from peptides forming amyloid fibrils. Phys Chem Chem Phys 2023; 25:23885-23893. [PMID: 37642522 DOI: 10.1039/d3cp01762a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Amyloids are cytotoxic protein aggregates that deposit in human tissues, leading to several health disorders. Their aggregates can also exhibit catalytic properties, and they have been used as candidates for the development of functional biomaterials. Despite being polymorphic, amyloids often assemble as cross-β fibrils formed by in-register β sheet layers. Recent studies of some amyloidogenic protein segments revealed that they crystallize as antiparallel out-of-register β sheets. Such arrangement has been proposed to be responsible for the cytotoxicity in amyloid diseases, however, there is still no consensus on the molecular mechanism. Interestingly, two amyloidogenic peptide segments, NFGAILS and FGAILSS, arrange into out-of-register and in-register β sheets, respectively, even though they solely differ by one aminoacid residue at both termini. In this work, we used density functional theory (DFT) to address how the strand register contributes into the packing and molecular properties of the NFGAILS and FGAILSS crystals. Our results show that the out-of-register structure is substantially more stable, at 0 K, than the in-register one due to stronger inter-strand contacts. Based on an analysis of the electrostatic potential of the crystal slabs, it is suggested that the out-of-register may potentially interact with negatively charged groups, like those found in cell membranes. Moreover, calculated reactivity descriptors indicate a similar outcome, where only the out-of-register peptide exhibits intrinsic reactive surface sites at the exposed amine and carboxylic groups. It is therefore suggested that the out-of-register arrangement may indeed be crucial for amyloid cytotoxicity. The findings presented here could help to further our understanding of amyloid aggregation, function, and toxicity.
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Affiliation(s)
- Camila Muñoz-Gutiérrez
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Box 721, Talca, Chile
| | - Francisco Adasme-Carreño
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile
- Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480112, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Box 721, Talca, Chile
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, Ciudad de México 09340, Mexico.
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Hosseini AN, van der Spoel D. Simulations of Amyloid-Forming Peptides in the Crystal State. Protein J 2023:10.1007/s10930-023-10119-3. [PMID: 37145206 DOI: 10.1007/s10930-023-10119-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
There still is little treatment available for amyloid diseases, despite their significant impact on individuals and the social and economic implications for society. One reason for this is that the physical nature of amyloid formation is not understood sufficiently well. Therefore, fundamental research at the molecular level remains necessary to support the development of therapeutics. A few structures of short peptides from amyloid-forming proteins have been determined. These can in principle be used as scaffolds for designing aggregation inhibitors. Attempts to this end have often used the tools of computational chemistry, in particular molecular simulation. However, few simulation studies of these peptides in the crystal state have been presented so far. Hence, to validate the capability of common force fields (AMBER19SB, CHARMM36m, and OPLS-AA/M) to yield insight into the dynamics and structural stability of amyloid peptide aggregates, we have performed molecular dynamics simulations of twelve different peptide crystals at two different temperatures. From the simulations, we evaluate the hydrogen bonding patterns, the isotropic B-factors, the change in energy, the Ramachandran plots, and the unit cell parameters and compare the results with the crystal structures. Most crystals are stable in the simulations but for all force fields there is at least one that deviates from the experimental crystal, suggesting more work is needed on these models.
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Affiliation(s)
- A Najla Hosseini
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE, 75124, Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE, 75124, Uppsala, Sweden.
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M Del Campo J, Ireta J. Understanding the unusual stiffness of hydrophobic dipeptide crystals. Phys Chem Chem Phys 2021; 23:11931-11936. [PMID: 33998612 DOI: 10.1039/d0cp06018f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The hydrophobic diphenylalanine peptide crystal is known to be unusually stiff, with an experimental Young's modulus in the range of 19-27 GPa. Here it is shown by means of density functional theory calculations that phenylalanine-leucine, leucine-phenylalanine, alanine-valine, valine-alanine and valine-valine hydrophobic dipeptide crystals are also unusually stiff, with Young's moduli in the range of 19.7-33.3 GPa. To further our understanding of the origin of that unusual stiffness, a linear correlation is established between Young's modulus and the strength and orientation of the hydrogen bond network developed along the crystals, showing that stiffness in these materials is primarily dictated by hydrogen bonding.
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Affiliation(s)
- Jorge M Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, C. P. 04510, Mexico.
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Rong C, Zhao D, Zhou T, Liu S, Yu D, Liu S. Homogeneous Molecular Systems are Positively Cooperative, but Charged Molecular Systems are Negatively Cooperative. J Phys Chem Lett 2019; 10:1716-1721. [PMID: 30916572 DOI: 10.1021/acs.jpclett.9b00639] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular systems bound together through noncovalent interactions are ubiquitous in nature, many of which are involved in essential life processes, yet little is known about the principles governing their structure, stability, and function. Cooperativity as one of the intrinsic properties in these systems plays a key role. In this work, on the basis of our recent quantification scheme of the cooperativity effect, we present a general pattern to identify which systems are positively cooperative and which are negatively cooperative. We show that cooperativity in homogeneous molecular systems is positive, but cooperativity in charged molecular systems is negative. We also employ analytical tools from energetics and information perspectives to appreciate the origin of the cooperativity effect. We find that positive cooperativity is dominated by the exchange-correlation interaction and steric effect, whereas negative cooperativity is governed by the electrostatic interaction. Our results should have strong implications for better understanding molecular recognition, protein folding, signal transduction, allosteric regulation, and other processes.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , People's Republic of China
| | - Tianjing Zhou
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Siyuan Liu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Donghai Yu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Shubin Liu
- Research Computing Center , University of North Carolina , Chapel Hill , North Carolina 27599-3420 , United States
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Rong C, Zhao D, Yu D, Liu S. Quantification and origin of cooperativity: insights from density functional reactivity theory. Phys Chem Chem Phys 2018; 20:17990-17998. [PMID: 29927447 DOI: 10.1039/c8cp03092h] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cooperativity is a widely used chemical concept whose existence is ubiquitous in chemical and biological systems but whose quantification is still controversial and origin much less appreciated. In this work, using the interaction energy of a molecular system, which is composed of multiple copies of a building block, we propose a quantitative measurement to evaluate the cooperativity effect. This quantification approach is then applied to six molecular systems, i.e., water cluster, argon cluster, protonated water cluster, zinc atom cluster, water cluster on top of a graphene sheet, and alpha helix of glycine amino acids, each with up to 20 copies of the building block. Cooperativity is seen in all these systems. Both positive and negative cooperativity effects are observed. Employing the two energy partition schemes in density functional theory and the information-theoretic quantities such as Shannon entropy, Fisher information, information gain, etc., we then examine the origin of the cooperativity effect for these systems. Strong linear correlations between the cooperativity measure and some of these theoretical quantities have been unveiled. With these correlations, we are able to quantitatively account for their origin of cooperativity. Our results show that the interactions governing the existence and validity of the cooperativity effect are complicated. An opposite mechanism in enthalpy-entropy compensation for positive and negative cooperativity has been unveiled. These results should provide new insights and understandings from a different viewpoint about the nature and origin of cooperativity to appreciate this vastly important chemical concept.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha Hunan 410081, P. R. China
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Nochebuena J, Cuautli C, Ireta J. Origin of cooperativity in hydrogen bonding. Phys Chem Chem Phys 2017; 19:15256-15263. [DOI: 10.1039/c7cp01695f] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bond cooperativity results from interactions between effective point dipoles which account for many-body contributions to cooperativity.
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Affiliation(s)
- Jorge Nochebuena
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México 09340
- Mexico
| | - Cristina Cuautli
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México 09340
- Mexico
| | - Joel Ireta
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México 09340
- Mexico
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Kulik HJ, Seelam N, Mar BD, Martínez TJ. Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness. J Phys Chem A 2016; 120:5939-49. [DOI: 10.1021/acs.jpca.6b04527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Heather J. Kulik
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Natasha Seelam
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Brendan D. Mar
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Todd J. Martínez
- Department
of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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