Research Article

The Infrared Absorption of Protein Molecules with α- helix Conformation and its Properties

Pang Xiao-feng
Institutes of Physical Electron and Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, P.R. China
*Corresponding author:

Pang Xiao-feng, Institutes of Physical Electron and Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, P.R. China, Email: pangxf2006@aliyun.com

Keywords:

Infrared absorption spectrum, Collagen, Bovine serum albumin, α-helix conformation, Soliton bio-energy transport

In order to investigate the relationship of molecular structure of protein molecules with its functions, we collected the infrared spectra of absorption of the collagen and bovine serum albumin containing α-helix conformation and their changes of strength of infrared absorption with varying temperature using the Perkin Elmer FT-IR and Nicolet Nexus FT-IR 670 spectrometer at room temperature of 250C in the region of 400-4000cm-1, respectively. The experimental results show that there is a new band of 1650cm-1 close to the conventional amide-I band of 1666cm-1 or 1670cm-1 and many other peaks for vibration of amide-I in the two protein molecules. In the meanwhile, the intensity of the new band decreases exponentially with increasing temperature and can be expressed by exp [-(0.437+ 8.987x10-6T2)], which resembles that in molecular crystal- acetanilide, but the intensity of 1666cm-1 band increases linearly. These results are first obtained from biological protein molecules. The 1650cm-1 anomalous band should be assigned to the soliton excitation, the 1666cm-1 band is related to the exciton in the systems according to the general rule. These conclusions can be explained and verified by using the theoretical results obtained from the soliton theory of bio-energy transport along the α-helix protein molecules with three channels. This suggests that there is the possibility of a nonlinear or soliton excitation in the collagen protein, and so on.

As it is known, the infrared spectra of protein molecules are closely related to their features of vibration, where its frequency of vibration is denoted by , where K is the force or elastic constant of the molecules and M is the effective mass of the oscillator. Then the infrared spectra are also related to properties of the structure of molecules. Thus we can use the properties of infrared spectra of absorption to have an insight into the properties of structure and conformation of protein molecules incorporating molecular functions. Therefore, the studies of infrared spectra of absorption of protein molecules have an important meaning in life sciences [1-7].

The vibration is an elementary form of motion of protein molecules, which has a characteristic infrared spectrum. There are, in general, thousands of vibrational modes even in a small protein molecule, their numbers of vibrational modes can be (3×(number of atoms ) –6). The frequencies of vibrational modes can be broadly distributed from approximately 4000cm-1 to a few cm-1 (collective modes of the entire protein) in the mid- to far- infrared frequencies. Generally speaking, strong force constants and small masses give rise to higher vibrational frequencies, such as O-C, O-H and N-H stretching, low frequency modes may be localized with weak force constants, such as bending, deformation and twisting motion of methyl groups, or globally collective motions with a large number of atoms. This means that different modes of vibration characterize really their functional states in the protein molecules, such as the low frequency collective modes are responsible for the directed flow of conformational energy for a variety of vital biological processes ranging from electron transfer [1] to enzyme action [2]; but stretching vibrations of C = 0 bond (amide) or amide-I in 1650 -1700cm-1 in the peptide groups of three α-helical protein molecules are responsible for the transport of bio-energy released by the hydrolysis of adenosine triphosphate (ATP) [8-12]. In this paper we will investigate in detail the properties of infrared spectra of absorption of collagen and bovine serum albumin (BSA) proteins with α-helical conformation, respectively.

   The collagen is a most common form of protein, and a main component in musculature in surface cells, for example, smooth muscle [13-16]. In the normal physiological condition it is a soft condensed matter, and resembles a solid state, which can still retain even though the temperature reach 95oC. The tropocollagen, a kind of collagen, is a fiber protein, which has a quaternary molecular-structure with superhelix made of three channel α-helix chains and containing a sugary side chain as shown in Fig.1. Each α- chain involves 1050 amino acid residues, in which the glycine is about 35%, proline 10%, hydro-proline 9% as well as some alumine and hydrolysin. Its one-dimensional (or primary) structure is a long chain made up of [Gly-X-Y]n as shown Fig.1c, where X and Y are proline and hydro-proline or hydrolysin, respectively. The secondary structure is a α-helical structure with a left-spin, which is formed by means of regular folding along the above one-dimensional main-chains. In such structure, the glycine is located at the center of the helix, the proline and hydro-proline are located on the exterior of the helix. If this secondary structure is further extended along the axial direction in the manner of left-hand helix, and is again folded as several helix-structures, then the tertiary structure of collagen is formed, in which the main chain is made up of several helices. If the above three long-chains are collected again together and wound each other in the manner of right-hand helix via linking by hydrogen bonds between the amide bond C=O and sub-amino group NH, i.e., C=O…NH, to form a fiber, this is just the quaternary structure of the collagen. In this structure the side-groups of two lysine residues contained in each peptide chain are linked by covalent bonds under the action of oxido-reductase of lynsin. Such a long chain can be represented by -CO-CH (NH) - CH2-CH2-CH2- CH = N-CH2- CH2- CH2-CH2- CH (NH) - CO-. Hence, the collagen is a kind of protein molecule having quaternary structure containing α-helical constitutions, in which the alternate arrangement of hydrogen bonds and covalent bonds plays an important role in stabilizing its structure, enhancing its tension strength and completing its biological-functions, such as the energy and information transports.

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Fig.1. The molecular structure of collagens: (a) fundamental structure of right α-helix with three channels. (b) atomic distribution on top section of three channel–axes, where G is carbon atom, is hydrogen bond, (c) one-dimensional structure of gly-pro-hydropro

Otherwise, BSA is an important component in the blood and is composed of α β structure, where α is α-helix type with three channels, β is β sheet [13-16].

We measured the infrared spectra of the type I-collagen using a Perkin Elmer spectrum GXFFIR spectrometer made in Germany equipped with a DTGS detector and having a resolution of 2cm-1, where the type I-collagens are extracted from the skin of a mouse and further purified by draining the water completely in our experiment, the light source used here is infrared silicon-carbon bars [17-21]. The collagens without water, which are completely drained, are sandwiched between KBr windows and transferred to a temperature cell in the infrared spectrometer. Their spectra of infrared absorption are recorded and performed in the range of 400-4000cm-1. To obtain an acceptable signal-to-noise ratio the 16 scans are used. The spectra of infrared absorption of the collagen from 400 to 4000cm-1 at 25℃ is shown in Fig.2, where the spectra lines at higher frequencies are dominated, which are generated by the vibrations of the amides. In the region of 1000-1800cm-1 there are two peaks at 1666.1cm-1 and 1680.4cm-1, which should be assigned to the vibrational modes of amide-I, but a new band at 1650.0cm-1 occurs also. At the same time, other amide bands, such as the amide-II band at 1542.1 cm-1, amide-III band at 1455.9cm-1 and 1404.5cm-1, amide-IV band at 1335.8cm-1 and 1243. 49cm-1 and amide-V band at 1081cm-1 in the range of 1000- 1500cm-1, are also found. Moreover, rich spectrum-lines in the range of 2800-4000cm-1, such as, 3433.2, 3408.0, 3389.7, 3355.6, 3296.3, 3244.1 and 3209.0cm-1, etc. Are observed as well.

In Fig. 3 we give the spectrum of infrared absorption of the collagen at the lower temperature, –1000C, by using this spectrometer. We see from this figure that many peaks of infrared absorption in Fig.2 occur.

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Fig.2. The infrared spectrum of the collagen from 400 to 4000cm-1 at 25 0C.


From Figs.2-3 we know clearly that (1) there are amide-II, III, IV, V bands, except for amide-I band in the spectra of infrared absorption of collagen; (2) a new band of 1650cm-1 appears really, which arise from the self- trapping of the vibrational quanta of amide-I, i.e., a soliton state occurs; (4) there are a lot of new peaks in collagen at low temperatures, which appear not at high temperatures. This result is possibly due to the fact that the high temperature suppresses some vibrational modes of amides in the protein molecules. 

The behaviors of the two bands of 1666cm-1 and 1650cm-1 are of great interests because they have important biological significances in biology, thus we will study them in details.

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Fig-3: infrared absorption spectra of collagen in the region of the amide-I mode at lower temperature –1000C.

The infrared spectra of the absorption of collagens at different temperatures are recorded, where the sample temperatures are varied from 15℃ to 95℃ in the intervals of 10℃ with a reported accuracy of ±1℃, which is controlled by the variable- temperature equipments, in which the water or water vapor is completely drained. The temperature-dependence of the intensity of infrared absorption at different temperature in the range of 15 – 950C are shown in Fig.4. This figure shows that the intensity of 1650 cm-1 band increases with decreasing temperature without apparent change in frequency and shape, but is only weakened at 95℃. On the contrary, the amide-I infrared absorption of 1666 cm-1 band decreases with decreasing temperature. The peak intensities of 1650 cm-1 and 1666 cm-1 bands versus the temperature are shown in Fig.5. Obviously, the temperature- dependences of intensities for the 1650cm-1 and 1666 cm-1 are different, the absorption intensity of 1666 cm-1 increases linearly with increasing temperature, but the intensity of 1650cm-1 decreases exponentially with increasing temperature, where the relation between them can be approximately simulated in an exponential form of I=I0exp {-[0.437+8.987x10-6 (T/0C)2]}, where T is represented by Celsius temperature, 0C is its unit, I0 is a constant related to the initial intensity. In Fig.5a we give the relationship between the logarithm of  relative intensity, Ln (I/I0), and temperature (T/0C)2 for the 1650cm-1 peak. Figure 5a shows that the experimental data of Ln (I/I0) = -[0.437+8.987x10-6 (T/0C)2] for the 1666cm-1 decreases linearly with increasing temperature of the medium. Figure 5b gives that the relative intensity, I/I0, for the 1666cm-1 really increases linearly with increasing the temperature of the medium. This is a new and interesting result.

In order to verify the real existences of 1666cm-1 and 1650cm-1 in the helix protein molecules we further measure and collect the infrared spectrum of absorption of BSA protein by the above method. Its infrared spectrum of absorption is shown in Fig. 6. From this figure we see that there are also 1671.04cm-1, 1660.34cm-1, 1650.75cm-1 1639.79 cm-1 in the range of 1600-1700cm-1. In accordance with the rules of assignment mentioned above, the 1671cm-1 should be the eigenfrequency of amide-I, the 1650 cm-1 denoted the band of the soliton in the BSA. These results are also similar to that in the collagen.

In order to confirm at the correctness of the above results, the infrared absorption spectra of collagen are subsequently measured and collected using the Nicolet Nexus FT-IR 670 spectrometer made in the USA. The results obtained are the same with the previous spectra. In this experiment, the water and the water vapor from the tested samples also are completely drained. Thus we believe that the above results are not affected by the accuracy of the instruments used and/or the water content in samples.

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From the above experiments we can obtain the following important conclusions:
 (1) The infrared absorption spectra of collagens are similar to those in the ACN [22], especially for the amide-I mode. An interesting result is that there are always the 1666cm-1 or 1671cm-1 and 1650cm-1 bands in the collagen and BSA. It is well known that the 1666cm-1 or 1671cm-1 is the eigenfrequency of vibration of amide-I, but the 1650 cm-1 is an anomalous band. In accordance of the Careri et.al [22] and J. C. Eilbeck et.al [23] and A. C. Scott’s conclusions [24] we should assign the 1666cm-1 or 1671cm-1 band to the vibrational excitation of amide-I (or exciton), but the1650 cm-1 band should be assigned to the soliton excitation in the collagen and BSA. Thus we have the reason to believe that there is the soliton excitation in these protein molecules.

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Fig.5. The temperature-dependences of intensity of infrared absorption of collagen in the region of 15 – 950C. (a) is the relationship of the relative intensity, Ln(I/I0), versus (T/0C)2 and the corresponding experiment data denoted by“●”for the 1650cm-1 peak, where the solid line expresses Ln(I/I0)= -[0.437+8.987x10-6(T/0C2)]. (b) represents the linear temperature - dependence of the relative intensity I/I0 for the 1666cm-1 peak .

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Fig.6. Infrared absorption spectra of BSA in the blood liquid .

(2) It is particularly interesting to be that the exponential rule of the temperature-dependence, exp {-[0.437+8.987x10-6 (T/K) 2]}, for the intensity of infrared absorption of 1650cm-1 bands were experimentally found in the collagen, which are shown in Figs. 4 and 5. It is coincident with the experimental result in ACN in the range of low temperatures of 10-280°K as well as with Alexander et al’s [25-27] and Pang’s [28-66] and Scott el. al’s [67-71] theoretical results of the soliton theory for the 1650cm-1 band in the acetanilide and proteins, which was represented by , where T is temperature of the system, a and b are some constants, but the linear increase of intensity of infrared absorption for 1666cm-1 band with increasing temperature in ACN and protein molecules, respectively. Thus, the theoretical results obtained by the soliton theory in the α-helical protein agree once again with the above experimental data of the collagen containing α-helical structure shown in Fig. 5. Thus we can affirm that there is the soliton excitation in the collagen proteins.

(3) It is quite clear from Figs. 2 and 3 that there are a lot of frequency bands in 400-4000cm-1 in the collagen, which can be also obtained and explained by the improved soliton-model of bio-energy transport probed by Pang in the α-helix proteins [16, 28-59]. In the new model we added a new coupling interaction between the acoustic phonon and amide-I vibrational modes,n X2(Un+1-Un)(B+n+1Bn+B+nBn+1) , into the Davydov’s Hamiltonian, and replaced the excitation state of a single particle with one exciton in the Davydov’s wave function by a quasi-coherent two- quantum state. Thus, the equation of motion and the properties of soliton in the improved model are completely different from that in the Davydov model, it eliminated the difficulties and problems of Davydov theory. The analytical results and numerical simulations in the new model show that the new soliton is thermally stable and has a enough long lifetime (about 10-10s) at 300°K in the α-helix protein, during its lifetime the soliton can transport over about 700-1000 amino acid residues. Thus the new soliton is possibly a carrier of bio-energy transport in biological processes[16, , 28-59].

We now calculate the vibrational - energy spectrum of amide-I in the α-helix proteins using the improved model. In this model the Hamiltonian and the wave function of the systems are represented by [28-32]

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G=53.71cm-1. These vibrational-energy levels of α-helix proteins obtained from Pang’s improved model[17-19] together with the experimental data of collagen are presented in Table 1 (only the energy-spectra at m=2 are given). It can be observed from Table 1 that these energy-bands at 1667cm-1, 1662cm-1, 1653cm-1, 1627cm-1 and 3204.71cm-1, 3218.19cm-1,3242.48cm-1, 3261.77cm-1, 3278.89cm-1, 3298.96cm-1, 3313.37cm-1, 3333.91cm-1and 3358.58 cm-1 are quite consistent with these peaks of 1680.31cm-1, 1666.11cm-1, 1650.01cm-1, 1624.92cm-1 and 3209.01cm-1, 3225.7cm-1,3244.04cm-1, 3262cm-1, 3278cm-1, 3296.33cm-1, 3316.2cm-1, 3333.18cm-1and 3355.58cm-1 occur in the infrared absorption spectra of the collagen in Figs. 2 and 3, respectively. This shows that there are soliton excitations in the collagen because these energy levels for the α-helical protein with three channels listed in Table 1 can only be obtained from the soliton theory of bio-energy transport by Pang[28-59]. Therefore, this agreement between the experimental data and theoretical results verify again the existence of the soliton excitation and the correctness of the improved theory of bio-energy transport in the collagen.

Table 1: Vibrational energy-spectra of α-helix protein molecules in cm-1

m

exp

cal

m

exp

cal

1

 

1610.95

1

 

1613.63

1

1624

1628.86

1

 

1631.37

1

1650

1653.98

1

1662

1661.98

1

1666

1668.14

1

1680

1679.32

2

3209

3212.56

2

 

3216.19

2

 

3218.91

2

 

3221.45

2

3225

3225.95

2

 

3230.21

2

 

3234.84

2

 

3235.49

2

3244

3245.48

2

 

3248.75

2

 

3254.68

2

 

3259.18

2

3262

3263.97

2

3267

3269.90

2

 

3269.99

2

 

3275.17

2

3278

3277.95

2

 

3280.19

2

 

3283.63

2

 

3284.11

2

 

3291.19

2

3296

3296.71

2

 

3302.34

2

 

3308.87

2

3316

3315.44

2

 

3321.69

2

 

3329.76

2

3333

3332.09

2

 

3342.15

2

 

3348.93

2

3355

3355.17

2

 

3359.91

2

 

3363.71

2

 

3363.97

2

3372

3371.54

2

 

3378.49

2

 

3381.66

2

 

3383.96

2

3389

3389.16

2

 

3393.91

2

 

3403.11

2

3408

3409.98

2

 

3415.64

2

 

3421.91

2

3433

3429.97

2

 

3440.08

2

3450

3450.14

2

3467

3452.64

From the above investigation of infrared spectra of absorption in collegen and BSA with α-helix conformation by using the Perkin Elmer FT-IR and Nicolet Nexus FT-IR 670 spectrometer in the region of 400-4000cm-1, respectively, we find a new band of 1650cm-1 close to the conventional amide-I band of 1666cm-1 and many spectrum peaks as well as the exponential rule of exp [-(0.437+ 8.987x10-6T2)] for the 1650cm-1 band and linearly temperature-dependence of intensity for the 1666cm-1 band, respectively. At the same time, we used the Pang’s soliton model to calculate the eigenenergy spectrum of α-helix protein molecules with three channels. In this energy spectrum these energy-bands at 1667cm-1, 1662cm-1, 1653cm-1, 1627cm-1 and 3204.71cm-1, 3218.19cm-1,3242.48cm-1, 3261.77cm-1, 3278.89cm-1, 3298.96cm-1, 3313.37cm-1, 3333.91cm-1and 3358.58 cm-1 are quite consistent with these peaks of 1680.31cm-1, 1666.11cm-1, 1650.01cm-1, 1624.92cm-1 and 3209.01cm-1, 3225.7cm-1,3244.04cm-1, 3262cm-1, 3278cm-1, 3296.33cm-1, 3316.2cm-1, 3333.18cm-1and 3355.58cm-1 occur in the infrared absorption spectra of the collagen in Figs. 2 and 3, respectively. These coincidences between the above experimental data and theoretical results exhibit and indicate clearly that there are really the soliton excitation, which is the carrier of bio-energy transport released in ATP hydrolysis, in the collagen containing α-helix structure. Thus we know that the functions of collagen relate closely to its α-helix structure of molecules and soliton excitation in it.

The author would like to acknowledge the financial support from the National project of China for (Grant No:2007CB936103).

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Published: 03 March 2017

Reviewed By : Dr. Zhuoyong Zhang, Dr. Maria Teresa Caccamo,

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