Patent Application
20230113585
The disclosure relates to a method and a computing system for estimating binding free energy of a mutant protein complex.
Conventionally, a wet-lab approach is adopted to study protein-protein interaction in a mutant protein complex. For example, a mutagenesis technique is utilized to change a specific amino acid residue of a wild-type protein complex to a mutant amino acid residue, thereby obtaining a mutant protein complex. Moreover, an isothermal titration calorimetry (ITC) technique is utilized to determine thermodynamic parameters of protein-protein interaction of the mutant protein complex, so as to determine the effect of amino acid mutations on protein-protein interaction. However, such approach requires extreme precautions for laboratory safety and extensive expertise, and is costly, labor intensive and time-consuming.
Therefore, an object of the disclosure is to provide a method and a computing system for estimating binding free energy of a mutant protein complex that can alleviate at least one of the drawbacks of the prior art.
According to one aspect of the disclosure, the method is to be implemented by a computing system. The method includes steps of:
According to another aspect of the disclosure, the computing system includes a storage device, an input module, an output module and a processor.
The storage device is configured to store amino acid structure data, amino acid physicochemical properties data and a model for estimating binding free energy. The amino acid structure data contains information related to properties of backbone dihedral angles, side-chain dihedral angles and bond rotation of amino acids. The amino acid physicochemical properties data contains information related to physicochemical properties of amino acids. The model for estimating binding free energy is implemented by a deep neural network.
The input module is configured to receive protein structure data that contains spatial coordinate sets of all atoms of a reference protein complex. The reference protein complex includes two wild-type protein chains.
The processor is electrically connected to the storage device, the input module and the output module. The processor is configured to obtain spatial coordinate sets respectively of all heavy atoms of the reference protein complex from the protein structure data. The processor is further configured to, for every two heavy atoms that belong respectively to the wild-type protein chains of the reference protein complex, calculate an Euclidean distance between the two heavy atoms as an interatomic distance based on the spatial coordinate sets respectively of the two heavy atoms. The processor is further configured to identify, based on the interatomic distances thus calculated, all interaction interfaces in the reference protein complex, wherein each of the interaction interfaces is between two residues respectively of the wild-type protein chains and wherein a distance between two α-carbons respectively of the residues is less than 5 Å. The processor is further configured to select one of the interaction interfaces that is related to a specific residue pair. The specific residue pair includes a specific residue at a site of interest in one of the wild-type protein chains of the reference protein complex and a paired residue in the other one of the wild-type protein chains of the reference protein complex. The processor is further configured to determine, according to information related to properties of side-chain dihedral angles and bond rotation of amino acids, a mutant residue that possibly results from mutation of the specific residue of the reference protein complex and that changes the reference protein complex into a mutant protein complex. The processor is further configured to obtain an inferred rotation angle that is related to a side chain of the specific residue of the reference protein complex from the amino acid structure data. The processor is further configured to calculate spatial coordinate sets respectively of all heavy atoms of the mutant residue based on the spatial coordinate sets of all heavy atoms of the specific residue of the reference protein complex and the inferred rotation angle. For a target interface between the mutant residue and a paired residue of the mutant protein complex that respectively correspond to the specific residue and the paired residue of the specific residue pair of the reference protein complex, the processor is further configured to, for every two heavy atoms respectively of the mutant residue and the paired residue of the mutant protein complex, calculate a value of atomic-level energy and an Euclidean distance based on the spatial coordinate sets of the heavy atoms of the reference protein complex and the spatial coordinate sets of the heavy atoms of the mutant residue of the mutant protein complex, and calculate, based on the values of atomic-level energy and the Euclidean distances thus calculated, an atomic distance related to the target interface and an atomic interaction of the target interface. The processor is further configured to obtain relevant information that is related to the specific residue of the reference protein complex and the mutant residue of the mutant protein complex from the amino acid physicochemical properties data. The processor is further configured to estimate binding free energy of the target interface by feeding, into the model for estimating binding free energy, the atomic distance related to the target interface, the atomic interaction of the target interface and the relevant information. The processor is further configured to control the output module to present the binding free energy of the target interface thus estimated.
Other features and advantages of the disclosure will become apparent in the following detailed description of the embodiment with reference to the accompanying drawings, of which:
Before the disclosure is described in greater detail, it should be noted that where considered appropriate, reference numerals or terminal portions of reference numerals have been repeated among the figures to indicate corresponding or analogous elements, which may optionally have similar characteristics.
Referring to
The computing system 100 includes a storage device 1, an input module 2, an output module 3 and a processor 4. The processor 4 is electrically connected to the storage device 1, the input module 2 and the output module 3.
The storage device 1 may be implemented by random access memory (RAM), double data rate synchronous dynamic random access memory (DDR SDRAM), read only memory (ROM), programmable ROM (PROM), flash memory, a hard disk drive (HDD), a solid state disk (SSD), electrically-erasable programmable read-only memory (EEPROM) or any other volatile/non-volatile memory devices, but is not limited thereto. The storage device 1 is configured to store amino acid structure data, amino acid physicochemical properties data and a model for estimating binding free energy.
The amino acid structure data reveals information related to properties of backbone dihedral angles, side-chain dihedral angles and bond rotation of amino acids. It is worth to note that in regard to amino acids of a protein chain (see
The amino acid physicochemical properties data contains information that is related to physicochemical properties of at least 21 amino acids, including alanine (i.e., Ala or A), arginine (i.e., Arg, R), asparagine (i.e., Asn or N), aspartate (i.e., Asp or D), cysteine (i.e., Cys or C), glutamine (i.e., Gln or Q) , glutamate (i.e., Glu or E), glycine (i.e., Gly or G), histidine (i.e., His or H), isoleucine (i.e., Ile or I), leucine (i.e., Leu or L), lysine (i.e., Lys or K), methionine (i.e., Met or M), phenylalanine (i.e., Phe or F), proline (i.e., Pro or P), serine (i.e., Ser or S), threonine (i.e., Thr or T), tryptophan (i.e., Trp or W) , tyrosine (i.e., Tyr or Y), valine (i.e., Val or V), and selenocysteine (i.e., Sec or U), but are not limited to what are disclosed herein. According to physicochemical properties of side chains of amino acids, the amino acids can be exemplarily classified into amino acids with positively or negatively charged side chains, amino acids with polar side chains, amino acids with hydrophobic side chains, and amino acids with special side chains. Physicochemical properties of amino acids can be exemplarily encoded by five bits of binary digits, wherein for the five bits from left to right, a first bit being “1” indicates an amino acid with a positively charged side chain, a second bit being “1” indicates an amino acid with a negatively charged side chain, a third bit being “1” indicates an amino acid with a polar side chain, a fourth bit being “1” indicates an amino acid with a hydrophobic side chain, and a fifth bit being “1” indicates an amino acid with a special side chain. For example, physicochemical properties of asparagine (N), which is an amino acid with a polar side chain, would be encoded by binary digits “00100”. Since physicochemical properties of amino acids have been well known to one skilled in the relevant art, detailed explanation of the same is omitted herein for the sake of brevity.
The model for estimating binding free energy is implemented by a deep neural network (DNN). Referring to
In one embodiment, the input module 2 is embodied using a network interface controller or a wireless transceiver that supports wireless communication standards, such as Bluetooth®) technology standards, Wi-Fi technology standards and/or cellular network technology standards. The input module 2 is connected to a telecommunications network (not shown) for receiving data transmitted by a remote device (e.g., a data server).
In one embodiment, the input module 2 is embodied using a keyboard, a mouse, or a touch panel that is configured to present a graphical user interface. However, it should be noted that implementations of the input module 2 are not limited to what are disclosed herein and may vary in other embodiments.
The input module 2 is configured to receive protein structure data that contains spatial coordinate sets respectively of all atoms of a reference protein complex which includes two wild-type protein chains. The spatial coordinate sets may be represented by a 3-tuple in a Cartesian coordinate system, but is not limited thereto.
The output module 3 may be embodied using a display device (e.g., a liquid-crystal display (LCD), a light-emitting diode (LED) display, a plasma display panel, a projection display or the like). However, implementation of the output module 3 is not limited to the disclosure herein and may vary in other embodiments.
The processor 4 may be implemented by a central processing unit (CPU), a microprocessor, a micro control unit (MCU), a system on a chip (SoC), or any circuit configurable/programmable in a software manner and/or hardware manner to implement functionalities discussed in this disclosure.
The processor 4 is configured to obtain, from the protein structure data, spatial coordinate sets respectively of all heavy atoms of the reference protein complex. A heavy atom is an atom other than hydrogen, such as oxygen, nitrogen or carbon. For every two heavy atoms that belong respectively to the wild-type protein chains of the reference protein complex, the processor 4 is configured to calculate an Euclidean distance between the two heavy atoms as an interatomic distance based on the spatial coordinate sets respectively of the two heavy atoms.
Subsequently, the processor 4 is configured to identify, based on the interatomic distances thus calculated, all interaction interfaces in the reference protein complex. Specifically, each of the interaction interfaces is between two residues respectively of the wild-type protein chains and a distance between two α-carbons (Cα) respectively of the residues is less than 5 Å.
Then, the processor 4 is configured to select one of the interaction interfaces that is related to a specific residue pair. The specific residue pair includes a specific residue at a site of interest in one of the wild-type protein chains of the reference protein complex and a paired residue in the other one of the wild-type protein chains of the reference protein complex.
Thereafter, the processor 4 is configured to determine, according to information related to properties of side-chain dihedral angles and bond rotation of amino acids, a mutant residue that possibly results from mutation of the specific residue of the reference protein complex and that changes the reference protein complex into a mutant protein complex.
Additionally, the processor 4 is configured to obtain an inferred rotation angle that is related to a side chain of the specific residue of the reference protein complex from the amino acid structure data.
The processor 4 is further configured to calculate spatial coordinate sets respectively of all heavy atoms of the mutant residue based on the spatial coordinate sets of all heavy atoms of the specific residue of the reference protein complex and based on the inferred rotation angle.
For example, Table 1 below shows a lookup table which exemplifies information contained in the amino acid structure data, wherein a symbol “Φ” represents a backbone dihedral angle that is an internal angle between two intersecting planes defined by chain “C - N - Cα - C”, a symbol “Ψ” represents a backbone dihedral angle that is an internal angle between two intersecting planes defined by chain “N - Cα - C -N”, a symbol “X1” represents a sidechain dihedral angle, and a symbol “ΔX1” represents an inferred rotation angle. The inferred rotation angle “ΔX1” can be determined based on the backbone dihedral angle “Φ”, the backbone dihedral angle “Ψ” and the sidechain dihedral angle “X1”.
In a scenario of determining an inferred rotation angle that is related to a side chain of an asparagine residue 501 (i.e., N501) of a wild-type spike protein where a backbone dihedral angle “Φ” is -60° (i.e., Φ = -60°), a backbone dihedral angle “Ψ” is -60° (i.e., Ψ = -60°), and a sidechain dihedral angle “X1” is 60° (i.e., X1 = -60°), four inferred rotation angles ΔX1 that are 60°, -120°, 180° and 0° (i.e., ΔX1 = 60°, -120°, 180° and 0°) can be obtained by looking up Table 1 above. Afterwards, the processor 4 is capable of calculating spatial coordinate sets respectively of all heavy atoms of a tyrosine residue 501 (i.e., Y501), which results from mutation of the spike protein, based on the four inferred rotation angles ΔX1 thus obtained and spatial coordinate sets of all heavy atoms of the asparagine residue 501 (N501). Specifically, for each of the four inferred rotation angles ΔX1, a group of spatial coordinate sets respectively of all heavy atoms of the tyrosine residue 501 is obtained; that is to say, four groups of spatial coordinate sets of all heavy atoms of the tyrosine residue 501 are obtained and correspond respectively to the four inferred rotation angles ΔX1. It is worth noting that an inferred rotation angle of 0 ° (i.e., ΔX1 = 0 °) means that a side chain of the mutant residue would not be rotated with respect to that of the specific residue (i.e., the asparagine residue 501).
For a target interface between the mutant residue and a paired residue of the mutant protein complex that respectively correspond to the specific residue and the paired residue of the specific residue pair of the reference protein complex, the processor 4 is configured to implement the following calculations. The processor 4 calculates, for every two heavy atoms respectively of the mutant residue and the paired residue of the mutant protein complex (hereinafter referred to as “a mutant-residue-paired-residue heavy atom pair”), a value of atomic-level energy and an Euclidean distance based on the spatial coordinate sets of the heavy atoms of the reference protein complex and the spatial coordinate sets of the heavy atoms of the mutant residue of the mutant protein complex, and calculates, based on the values of atomic-level energy and the Euclidean distances thus calculated, an atomic distance (D) related to the target interface and an atomic interaction force (E) of the target interface.
Specifically, the processor 4 is configured to calculate, for each mutant-residue-paired-residue heavy atom pair of the mutant protein complex, the value of atomic-level energy as a sum of values of Van der Waals force, hydrogen bond, π-π stacking interaction and electrostatic force between the two heavy atoms of the pair. Thereafter, the processor 4 is further configured to calculate the atomic distance (D) as an average of the Euclidean distances of all mutant-residue-paired-residue heavy atom pairs of the mutant protein complex, and to calculate the atomic interaction force (E) as a sum of the values of atomic-level energy of all mutant-residue-paired-residue heavy atom pairs of the mutant protein complex.
Mathematically, the atomic distance (D) and the atomic interaction force (E) can be respectively expressed by
where N is a total number of the mutant-residue-paired-residue heavy atom pairs of the mutant protein complex, di represents an Euclidean distance of an ith one of the mutant-residue-paired-residue heavy atom pairs of the mutant protein complex, and ei represents an atomic-level energy of an ith one of the mutant-residue-paired-residue heavy atom pairs of the mutant protein complex. Since calculations of Van der Waals force, hydrogen bond, π-π stacking interaction and electrostatic force have been well known to one skilled in the relevant art, detailed explanation of the same is omitted herein for the sake of brevity.
It should be noted that in a scenario where multiple inferred rotation angles are obtained and multiple groups of spatial coordinate sets of all heavy atoms of a mutant residue are thereby calculated, the processor 4 would eventually calculate, respectively for the multiple groups of spatial coordinate sets, multiple pairs of the atomic distance (D) and the atomic interaction force (E) (hereinafter also referred to as multiple candidates). Then, the processor 4 would reserve one of the multiple candidates, in which the atomic interaction force (E) is the smallest among the atomic interaction forces (E) of the candidates, for further processing.
Referring to the previous example where the four inferred rotation angles (ΔX1 = 60°, -120°, 180° and 0°) are respectively used to calculate four groups of spatial coordinate sets of all heavy atoms of the tyrosine residue 501, the processor 4 would eventually calculate, respectively for the four groups of spatial coordinate sets, four pairs of the atomic distance and the atomic interaction force (D1, E1), (D2, E2), (D3, E3) and (D4, E4) that respectively correspond to the four inferred rotation angles (ΔX1 = 60°, -120°, 180° and 0°). When the atomic interaction force (E4) is the smallest among the atomic interactions forces (El, E2, E3 and E4), the processor 4 would reserve the pair of the atomic distance and the atomic interaction force (D4, E4) for further processing.
The processor 4 is further configured to obtain relevant information that is related to the specific residue of the reference protein complex and the mutant residue of the mutant protein complex from the amino acid physicochemical properties data.
The processor 4 is further configured to estimate binding free energy of the target interface by feeding, into the model for estimating binding free energy, the atomic distance (D) related to the target interface, the atomic interaction force (E) of the target interface and the relevant information. The input layer of the model for estimating binding free energy is configured to receive the atomic distance (D), the atomic interaction force (E) and the relevant information, and the output layer of the model for estimating binding free energy is configured to output the binding free energy thus estimated.
It should be noted that the model for estimating binding free energy is trained in advance by using a plurality of training sets that respectively correspond to a plurality of training protein complexes. The training protein complexes are obtained by a computer over the Internet from a protein database such as “SKEMPI”, “AB-Bind”, “PROXIMATE” or “dbMPIKT”. Each of the training protein complexes includes at least one pair of training residues that are respectively in two protein chains of the training protein complex and that are related to a training interaction interface. Each of the training sets contains, for each of the at least one pair of training residues included in the corresponding one of the training protein complexes, an atomic distance that is related to the training interaction interface to which the pair of training residues are related, an atomic interaction force of the training interaction interface to which the pair of training residues are related, binding free energy of the training interaction interface to which the pair of training residues are related, and information related to physicochemical properties of amino acids that are related to the pair of training residues. After the model for estimating binding free energy has been trained by feeding the training sets thereinto, performance of the model for estimating binding free energy can be validated by using a plurality of validation sets, wherein contents of the validation sets are similar to those of the training sets.
Referring to
Finally, the processor 4 is configured to control the output module 3 to present the binding free energy of the target interface thus estimated. A person in the relevant art is able to analyze the mutant protein complex according to the binding free energy presented by the output module 3.
It should be noted that the lower the binding free energy, the stronger a binding force between two residues. Therefore, binding free energy of an interface between two residues respectively of two protein chains of a protein complex indicates how much binding force the two residues exert to bind the two protein chains together so as to stabilize the protein complex.
Moreover, when a specific residue of a wild-type protein complex is mutated and the wild-type protein complex becomes a mutant protein complex, binding free energy calculated for the mutant protein complex is helpful to determining how much impact the mutation has on functions of the wild-type protein complex.
With regards to drug design, for a predetermined interaction interface that is related to a protein of interest, a drug may be designed, with the assistance of the computing system 100 according to the disclosure, to favorably and exclusively bind to the protein of interest. In this way, efficiency and a success rate of drug development may be improved.
Referring to
In step S61, the processor 4 of the computing system 100 obtains, from the protein structure data, spatial coordinate sets respectively of all heavy atoms of the reference protein complex. For every two heavy atoms that belong respectively to the wild-type protein chains of the reference protein complex, the processor 4 calculates an Euclidean distance between the two heavy atoms as an interatomic distance based on the spatial coordinate sets respectively of the two heavy atoms.
In step S62, the processor 4 identifies, based on the interatomic distances calculated in S61, all interaction interfaces in the reference protein complex.
In step S63, the processor 4 selects one of the interaction interfaces that is related to a specific residue pair, wherein the specific residue pair includes a specific residue at a site of interest in one of the wild-type protein chains of the reference protein complex and a paired residue in the other one of the wild-type protein chains of the reference protein complex.
In step S64, the processor 4 determines, according to information related to properties of side-chain dihedral angles and bond rotation of amino acids, a mutant residue that possibly results from mutation of the specific residue of the reference protein complex and that changes the reference protein complex into a mutant protein complex. Subsequently, the processor 4 obtains, from the amino acid structure data, an inferred rotation angle that is related to a side chain of the specific residue of the reference protein complex, and calculates spatial coordinate sets respectively of all heavy atoms of the mutant residue based on the inferred rotation angle and the spatial coordinate sets of all heavy atoms of the specific residue of the reference protein complex.
In step S65, for a target interface between the mutant residue and a paired residue of the mutant protein complex that respectively correspond to the specific residue and the paired residue of the specific residue pair of the reference protein complex, the processor 4 calculates, for every two heavy atoms respectively of the mutant residue and the paired residue of the mutant protein complex (hereinafter referred to as “a mutant-residue-paired-residue heavy atom pair”), a value of atomic-level energy and an Euclidean distance based on the spatial coordinate sets of the heavy atoms of the reference protein complex and the spatial coordinate sets of the heavy atoms of the mutant residue of the mutant protein complex, and calculates, based on the values of atomic-level energy and the Euclidean distances thus calculated, an atomic distance (D) related to the target interface and an atomic interaction force (E) of the target interface.
In particular, the processor 4 calculates, for each mutant-residue-paired-residue heavy atom pair of the mutant protein complex, the value of atomic-level energy as a sum of values of Van der Waals force, hydrogen bond, π-π stacking interaction and electrostatic force between the two heavy atoms of the mutant-residue-paired-residue heavy atom pair. The processor 4 calculates the atomic distance (D) as an average of the Euclidean distances of all mutant-residue-paired-residue heavy atom pairs of the mutant protein complex. The processor 4 calculates the atomic interaction force (E) as a sum of the values of atomic-level energy of all mutant-residue-paired-residue heavy atom pairs of the mutant protein complex.
Further, the processor 4 obtains, from the amino acid physicochemical properties data, relevant information that is related to the specific residue of the reference protein complex and the mutant residue of the mutant protein complex.
In step S66, the processor 4 estimates binding free energy of the target interface by feeding, into the model for estimating binding free energy, the atomic distance (D) related to the target interface, the atomic interaction force (E) of the target interface and the relevant information.
To sum up, for the method and the computing system 100 according to the disclosure, a dry-lab approach is adopted to estimate binding free energy of a mutant protein complex. For a target interface between a mutant residue and a paired residue of a mutant protein complex, an atomic distance and an atomic interaction force are calculated based on the protein structure data that contains spatial coordinate sets respectively of all atoms of a reference protein complex, and on the amino acid structure data that contains information related to properties of backbone dihedral angles, side-chain dihedral angles and bond rotation of amino acids. Thereafter, the model for estimating binding free energy, which is implemented by a deep neural network, is utilized to estimate binding free energy of the target interface based on the atomic distance, the atomic interaction force, and relevant information that is related to physicochemical properties of the mutant residue of the mutant protein complex and a specific residue, which corresponds to mutant residue, of the reference protein complex. In this way, binding free energy of a mutant protein complex may be efficiently and accurately estimated without conducting biochemical experimentation.
In the description above, for the purposes of explanation, numerous specific details have been set forth in order to provide a thorough understanding of the embodiment. It will be apparent, however, to one skilled in the art, that one or more other embodiments may be practiced without some of these specific details. It should also be appreciated that reference throughout this specification to “one embodiment,” “an embodiment,” an embodiment with an indication of an ordinal number and so forth means that a particular feature, structure, or characteristic may be included in the practice of the disclosure. It should be further appreciated that in the description, various features are sometimes grouped together in a single embodiment, figure, or description thereof for the purpose of streamlining the disclosure and aiding in the understanding of various inventive aspects, and that one or more features or specific details from one embodiment may be practiced together with one or more features or specific details from another embodiment, where appropriate, in the practice of the disclosure.
While the disclosure has been described in connection with what is considered the exemplary embodiment, it is understood that this disclosure is not limited to the disclosed embodiment but is intended to cover various arrangements included within the spirit and scope of the broadest interpretation so as to encompass all such modifications and equivalent arrangements.
This application claims priority of U.S. Provisional Pat. Application No. 63/248804, filed on Sep. 27, 2021.
| Number | Date | Country | |
|---|---|---|---|
| 63248804 | Sep 2021 | US |
