It depends on the particular protease and cooking temperature.
From (Santé-Lhoutellier 2008):
Meat cooking affected myofibrillar protein susceptibility to proteases, with increased or decreased rates, depending on the nature of the protease and the time/temperature parameters. Results showed a direct and quantitative relationship between protein carbonylation (p < 0.01) and aggregation (p < 0.05) induced by cooking and proteolytic susceptibility to pepsin. However, no such correlations have been observed with trypsin and α-chymotrypsin.
The change of an amino group by a carbonyl group can modify the redox properties of proteins and so can disturb the recognition of proteins by proteases.
From (Bax 2012), an in vitro study:
At 70 °C, the proteins underwent denaturation that enhanced the speed of pepsin digestion by increasing enzyme accessibility to protein cleavage sites. Above 100 °C, oxidation-related protein aggregation slowed pepsin digestion but improved meat protein overall digestibility.
From (Bax 2013), an in vivo study on "the effect of meat cooking temperature on the parameters of protein digestion in the small intestine, using the minipig as a model animal":
An in vitro approach has revealed that cooking temperature is one of the key determinants of digestion speed. Relative to raw meat, the speed of digestion was increased at a cooking temperature of 70°C, and decreased at a cooking temperature above 100°C. (Summarizing the previous study.)
This effect was explained by a progressive denaturation of proteins, which exposes cleavage sites to digestive enzymes, at low temperatures, and oxidation leading to protein aggregation, which hides cleavage sites, at high temperatures.
[I]n the present study, very similar variations to those recorded in vitro were observed, with the highest speed of digestion observed at a cooking temperature of 75°C.
This study shows that the speed of protein digestion, a parameter of increasing interest in nutrition, can be modulated by meat preparation, a slower digestion being observed with high cooking temperature.
Marie-Laure Bax, Laurent Aubry, Claude Ferreira, Jean-Dominique Daudin, Philippe Gatellier, Didier Rémond, and Véronique Santé-Lhoutellier. Cooking Temperature Is a Key Determinant of in Vitro Meat Protein Digestion Rate: Investigation of Underlying Mechanisms. Journal of Agricultural and Food Chemistry 2012 60 (10), 2569-2576
Bax M-L, Buffière C, Hafnaoui N, Gaudichon C, Savary-Auzeloux I, et al. (2013) Effects of Meat Cooking, and of Ingested Amount, on Protein Digestion Speed and Entry of Residual Proteins into the Colon: A Study in Minipigs. PLoS ONE 8(4): e61252. doi:10.1371/journal.pone.0061252
Veronique Santé-Lhoutellier, Thierry Astruc, Penka Marinova, Eleonore Greve, and Philippe Gatellier. Effect of Meat Cooking on Physicochemical State and in Vitro Digestibility of Myofibrillar Proteins. Journal of Agricultural and Food Chemistry 2008 56 (4), 1488-1494