classdef MyClass < handle

   properties

   % big matrices
       M1; %sparse
       M2;
       M3;

   end %properties

    methods

       function obj = MyClass(...)
          ...
          obj.InitializeM1(...);
          obj.CreateM2(...);
          ...
       end

       function Heavy(obj)
         ....
         for i=1:N
             obj.M3(:,i) = obj.UseM1(obj.M2(:,i))
         end

       end % Heavy

      function out = UseM1(in)
            %....
      end % UseM2

    end % methods

end % MyClass

parfor i=1:N
     tmp(:,i) = UseM2(obj,obj.M2(:,i))
 end
 obj.M3 = tmp;