To date, there has been no study of protein molecular structures affected by bioethanol processing in relation to protein nutritive values of the new co-products of bioethanol production. The objective of the present study was to investigate the relationship between protein molecular structures (in terms of protein α-helix and β-sheet spectral intensity and their ratio and amide I to amide II spectral intensity and their ratio) and protein rumen degradation kinetics (rate and extent), estimated protein intestinal digestibility and total truly absorbed protein in small intestine (metabolisable protein) in different types of dried distillers grains with solubles (DDGS), such as wheat DDGS, maize DDGS and blend DDGS (wheat:maize = 70:30). The protein molecular structures of the different types of DDGS affected by processing were identified using diffuse reflectance IR Fourier transform spectroscopy. The results showed that the protein structure α-helix to β-sheet ratio in the DDGS had a strongly negative correlation with estimated intestinal digestibility of ruminally undegraded protein (%dRUP, R − 0·95, P = 0·04), tended to have a significant correlation with the protein PC subfraction (which was undegradable and contained proteins associated with lignin and tannins and heat-damaged proteins) (R 0·91, P = 0·09) and had no correlation (P>0·10) with rumen degradation kinetics (rate and extent), total intestinally absorbed protein supply and degraded protein balance. However, the protein amide I to amide II ratio in the DDGS had a strongly positive correlation with soluble crude protein (CP) (R 0·99, P < 0·01), protein PA subfraction (which was instantaneously solubilised at time zero) (R 0·99, P < 0·01), protein PB2 subfraction (which was intermediately degradable) (R − 0·95, P = 0·04) and total digestible CP (R 0·95, P = 0·04). The amide I to amide II ratio also had strongly negative correlations with ruminally undegraded protein (%RUP: R − 0·96, P = 0·03) and the degraded protein balance (OEB: R − 0·97, P = 0·02), but had no correlation (P>0·10) with the total intestinally absorbed protein supply. Multiple regression results show that the protein structure α-helix to β-sheet ratio was a better predictor of %dRUP with R2 0·92. The amide I to II ratio was a better predictor of the degraded protein balance with R2 0·93 in the DDGS. In conclusion, the changes in the protein molecular structure α-helix to β-sheet ratio and the amide I to amide II ratio during bioethanol processing (either due to fermentation processing or due to heat drying) were highly associated with estimated protein intestinal digestibility and degraded protein balance, but were not associated with total intestinally absorbed protein supply from the DDGS to dairy cattle. The present study indicates that a potential novel method could be developed based on the protein molecular structure parameters to improve the estimation of protein value after a validation in a large-scale in vivo study is done.