Article ; Online: Refining protein amide I spectrum simulations with simple yet effective electrostatic models for local wavenumbers and dipole derivative magnitudes.
Physical chemistry chemical physics : PCCP
2024 Volume 26, Issue 2, Page(s) 1166–1181
Abstract: Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is ... ...
| Abstract | Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures - α-helices, parallel and antiparallel β-sheets - with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the CO bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment. |
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| MeSH term(s) | Amides/chemistry ; Static Electricity ; Models, Molecular ; Proteins/chemistry ; Spectrophotometry, Infrared/methods |
| Chemical Substances | Amides ; Proteins |
| Language | English |
| Publishing date | 2024-01-03 |
| Publishing country | England |
| Document type | Journal Article |
| ZDB-ID | 1476244-4 |
| ISSN | 1463-9084 ; 1463-9076 |
| ISSN (online) | 1463-9084 |
| ISSN | 1463-9076 |
| DOI | 10.1039/d3cp02018e |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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